相关论文: Ligand Discrimination in Myoglobin from Linear-Sca…
A significant amount of protein function requires binding small molecules, including enzymatic catalysis. As such, designing binding pockets for small molecules has several impactful applications ranging from drug synthesis to energy…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
The bandgap and band bowing parameter of semiconductor alloys are calculated with a fast and realistic approach. The method is a dielectric scaling approximation that is based on a scissor approximation. It adds an energy shift to the…
Cell membranes phase separate into ordered ${\rm L_o}$ and disordered ${\rm L_d}$ domains depending on their compositions. This membrane compartmentalization is heterogeneous and regulates the localization of specific proteins related to…
The most important function of proteins may well be to bind to other biomolecules. It has long been felt that kinetic rates of bond formation and dissociation between soluble receptors and ligands might account for most features of the…
Quantum--Mechanical methods that are both computationally fast and accurate are not yet available for electronic excitations having charge transfer character. In this work, we present a significant step forward towards this goal for those…
We investigate diffusion-limited reactions between a diffusing particle and a target site on a semiflexible polymer, a key factor determining the kinetics of DNA-protein binding and polymerization of cytoskeletal filaments. Our theory…
The essential features of the in vitro refolding of myoglobin are expressed in a solvable physical model. Alpha helices are taken as the fundamental collective coordinates of the system, while the refolding is assumed to be mainly driven by…
Semi-local DFT methods exhibit significant errors for the phase diagrams of transition-metal oxides that are caused by an incorrect description of molecular oxygen and the large self-interaction error in materials with strongly localized…
The band structures and optical properties of monoclinic HfO2 are investigated by the local density approximation (LDA)+U approach. With the on-site Coulomb interaction being introduced to 5d orbitals of Hf atom and 2p orbitals of O atom,…
The percentage and sequence of AT and GC base pairs and charges on the DNA backbone contribute significantly to the stiffness of DNA. This elastic property of DNA also changes with small interacting ligands. The single-molecule force…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
The lowest-lying states of LiH have been widely used to develop and calibrate many different methods in quantum mechanics. In this paper we show that the electron-transfer processes occurring in these two states are a difficult test for…
Accurate prediction of drug-target binding affinity can accelerate drug discovery by prioritizing promising compounds before costly wet-lab screening. While deep learning has advanced this task, most models fuse ligand and protein…
We study the dopant-induced inhomogeneity effect on the electronic properties of heavy fermionCeCoIn5using a combined approach of density functional theory (DFT) and dynamical mean-field theory (DMFT). The inhomogeneity of the hybridization…
The systematic trends in structural and electronic properties of perylene diimide (PDI) derived dye molecules have been investigated by DFT calculations based on projector augmented wave (PAW) method including gradient corrected…
Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the…
The self-assembly of submonolayer amounts of Au on the densely stepped Si(553) surface creates an array of closely spaced \atomic wires" separated by 1.5 nm. At low temperature, charge transfer between the terraces and the row of silicon…
Dynamical Mean-Field Theory (DMFT) has established itself as a reliable and well-controlled approximation to study correlation effects in bulk solids and also two-dimensional systems. In combination with standard density-functional theory…