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Molecular docking is a central method in the computer-based screening of compound libraries as a part of the rational approach to drug design. Although the method has proved its competence in predicting binding modes correctly, its inherent…
A novel combination of discontinuous molecular dynamics and the Langevin equation, together with an intermediate-resolution model, are used to carry out long (several $\mu$s) simulation and study folding transition and transport of proteins…
Density functional theory (DFT) has been widely applied to a variety of realistic materials but often struggles to explain the properties of correlated systems. The DFT + U method, which introduces a Hubbard U correction to the DFT, has…
Macromolecular crowding affects biophysical processes as diverse as diffusion, gene expression, cell growth, and senescence. Yet, there is no comprehensive understanding of how crowding affects reactions, particularly multivalent binding.…
Strong shear thickening and jamming in dense suspensions are driven by friction as particles are sheared into contact. Control over these frictional interactions can be achieved via particle shape and roughness, and also via the particles'…
The specificity of molecular recognition is important to molecular self-organization. A prominent example is the biological cell where, within a highly crowded molecular environment, a myriad of different molecular receptor pairs recognize…
The interaction within a hybrid system consisting of a spherical metal nanoparticle and a nearby organic dye molecule is formulated in a combined quantum-classical approach. Whereas the nanoparticle's polarization field is treated in…
Molecular docking is a key task in computational biology that has attracted increasing interest from the machine learning community. While existing methods have achieved success, they generally treat each protein-ligand pair in isolation.…
Dynamical mean field theory (DMFT) combined with the local density approximation (LDA) is widely used in solids to predict properties of correlated systems. In this paper, its application to one of the simplest strongly correlated systems,…
Biological membranes are elastic media in which the presence of a transmembrane protein leads to local bilayer deformation. The energetics of deformation allow two membrane proteins in close proximity to influence each other's equilibrium…
This is a follow-up of our recently proposed work on pseudopotential calculation (Ref. [21]) of atoms and molecules within DFT framework, using cartesian coordinate grid. Detailed results are presented to demonstrate the usefulness,…
Density functional theory (DFT) within the local density approximation (LDA) is used to understand the electronic properties of Na1/3CoO2 and Na1/3CoO2(H2O)4/3, which was recently found to be superconducting1. Comparing the LDA charge…
The ytterbium monohydroxide is a promising molecule for a new physics searches. It is well known that levels of the opposite parity, separated by the energy split, so-called $l$-doublets, define the experimental electric field strength…
A density functional theory (DFT) approach to computing transition metal oxide heat of formation without adjustable parameters is presented. Different degrees of $d$-electron localization in oxides are treated within the DFT+$U$ approach…
We study theoretically the thermodynamics, over a broad temperature range (5 C to 125 C), related to hydrated water upon protein unfolding. The hydration effect is modeled as interacting dipoles in an external field, mimicking the influence…
We calculate bending moduli along the principal directions for thirty-two select atomic monolayers using ab initio Density Functional Theory (DFT). Specifically, considering representative materials from each of Groups IV, V, III-V…
We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the…
Polymorphs in molecular crystals are often very close in energy, yet they may possess markedly different physical and chemical properties. The understanding and prediction of polymorphism is of paramount importance for a variety of…
A structural model of hydrogenated amorphous silicon containing an isolated dangling bond is used to investigate the effects of electron interactions on the electronic level splittings, localization of charge and spin, and fluctuations in…
With a view towards optimizing gas storage and separation in crystalline and disordered nanoporous carbon-based materials, we use ab initio density functional theory calculations to explore the effect of chemical functionalization on gas…