Membrane protein folding in the viscous microenvironment of a lipid bilayer is an inherently slow process that challenges experiments and computational efforts alike. The folding kinetics is moreover associated with topological modulations of the bio...
During the drug discovery and design process, the acid-base dissociation constant (pKa) of a molecule is critically emphasized due to its crucial role in influencing the ADMET (absorption, distribution, metabolism, excretion, and toxicity) properties...
Intrinsically disordered proteins and protein regions (IDPs/IDRs) carry out important biological functions without relying on a single well-defined conformation. As these proteins are a challenge to study experimentally, computational methods play im...
MOTIVATION: Coding and noncoding RNA molecules participate in many important biological processes. Noncoding RNAs fold into well-defined secondary structures to exert their functions. However, the computational prediction of the secondary structure f...
Several enhanced sampling techniques rely on the definition of collective variables to effectively explore free energy landscapes. The existing variables that describe the progression along a reactive pathway offer an elegant solution but face a numb...
BACKGROUND: Dapsone (DAP) is an anti-inflammatory and antimicrobial active pharmaceutical ingredient used to treat, e.g., AIDS-related diseases. However, low solubility is a feature hampering its efficient use.
Cluster expansion (CE) provides a general framework for first-principles-based theoretical modeling of multicomponent materials with configurational disorder, which has achieved remarkable success in the theoretical study of a variety of material pro...
We propose a scheme for ab initio configurational sampling in multicomponent crystalline solids using Behler-Parinello type neural network potentials (NNPs) in an unconventional way: the NNPs are trained to predict the energies of relaxed structures ...
Predicting the structural properties of water and simple fluids confined in nanometer scale pores and channels is essential in, for example, energy storage and biomolecular systems. Classical continuum theories fail to accurately capture the interfac...
Fast evolution of modern society stimulates intense development of new materials with novel functionalities in energy and environmental applications. Due to rapid progress of computer science, computational design of materials with target properties ...