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Tailoring the functional properties of advanced organic/inorganic heterogeonous devices to their intended technological applications requires knowledge and control of the microscopic structure inside the device. Atomistic quantum mechanical…
We employ a multiple scattering expansion to systematically derive curvature corrections to the Casimir-Polder (CP) interaction between small an-isotropic particles and general magneto-dielectric surfaces. Our results, validated against…
Accurate estimation of mutational effects on protein-protein binding energies is an open problem with applications in structural biology and therapeutic design. Several deep learning predictors for this task have been proposed, but,…
It has been established that Terahertz (THz) band signals can interact with biomolecules through resonant modes. Specifically, of interest here, protein activation. Our research goal is to show how directing the mechanical signaling inside…
Small molecules that interact strongly with water were the subject of this molecular dynamics (MD) study. These solutes include a cryoprotectant (DMSO), a polyalcohol [CH$_2$(OH)$_2$], carboxylic acid conjugates (HCOOH and HCOONa), an…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
Nanoscientists have long conjectured that adjacent nanoparticles aggregate with one another in certain preferential directions during a chemical synthesis of nanoparticles, which is referred to the oriented attachment. For the study of the…
In this review article, we focus on emerging nanocantilever based biological sensors and discuss the response of nanocantilevers towards bio-molecules capture. The article guides the reader through various modes of operation (e.g., static…
Alignment of molecules through electric fields minimizes the averaging over orientations, e. g., in single particle imaging experiments. The response of molecules to external ac electric fields is governed by their polarizability tensor,…
Continuum or hybrid modeling of bilayer membrane morphological dynamics induced by embedded proteins necessitates the identification of protein-membrane interfaces and coupling of deformations of two surfaces. In this article we developed…
We present a coarse-grained C$\alpha$-based protein model that can be used to simulate structured, intrinsically disordered and partially disordered proteins. We use a Go-like potential for the structured parts and two different variants of…
Poisson-Boltzmann theory is the cornerstone for soft matter electrostatics. We provide novel exact analytical solutions to this non-linear mean-field approach, for the diffuse layer of ions in the vicinity of a planar or a cylindrical…
We reproduced the initial sticking probability of O$_{2}$/Al(111) by use of spin-polarized density functional theory and quantum dynamics calculations. We found a large activation barrier when the molecule is dissociatively adsorbed through…
Near-critical binary mixtures containing ions and confined between two charged and selective surfaces are studied within a Landau-Ginzburg theory extended to include electrostatic interactions. Charge density profiles and the effective…
Inverse Protein Folding (IPF) is a critical subtask in the field of protein design, aiming to engineer amino acid sequences capable of folding correctly into a specified three-dimensional (3D) conformation. Although substantial progress has…
Fluorescent molecules emit light in a dipole radiation pattern that can be used to infer their orientation through defocused fluorescence microscopy. Proper measurement of the orientation requires mathematical modeling of the radiation…
The interplay of membrane proteins is vital for many biological processes, such as cellular transport, cell division, and signal transduction between nerve cells. Theoretical considerations have led to the idea that the membrane itself…
We present a set of Langmuir binding models in which electrostatic cooperativity effects to protein sorption is incorporated in the spirit of Guoy-Chapman-Stern models, where the global substrate (microgel) charge state is modified by bound…
Prediction of metabolism in cytochrome P450s remains to be a crucial yet challenging topic in discovering and designing drugs, agrochemicals and nutritional supplements. The problem is challenging because the rate of P450 metabolism depends…
Based on recent studies on hydrophobic interactions, it is devoted to investigate the directional nature of hydrophobic interactions. It means that the hydrophobic interactions are dependent on the relative orientations as the solutes tend…