Related papers: Charge Transfer Database for Bio-molecule Tight Bi…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…
We apply a first-principles computational approach to study a light-sensitive molecular switch. The molecule that comprises the switch can convert between a trans and a cis configuration upon photo-excitation. We find that the conductance…
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…
Protein machines often exhibit long range interplay between different sites in order to achieve their biological tasks. We investigate and characterize the non--linear energy localization and the basic mechanisms of energy transfer in…
Spin crossover (SCO) complexes are highly promising candidates for a myriad of potential applications in room-temperature electronics; however, as it stands, establishing a clear connection between their spin-state switching and transport…
We systematically examine all the tight-binding parameters pertinent to charge transfer along DNA. The $\pi$ molecular structure of the four DNA bases (adenine, thymine, cytosine, and guanine) is investigated by using the linear combination…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
The ultrafast dynamics of charge carriers in organic donor-acceptor interfaces are of primary importance to understanding the fundamental properties of these systems. In this work, we focus on a charge-transfer complex formed by…
Proteins are an important class of biomolecules that serve as essential building blocks of the cells. Their three-dimensional structures are responsible for their functions. In this thesis we have investigated the protein structures using a…
Engineering systems modelling and analysis based on the bond graph approach has been applied to biomolecular systems. In this context, the notion of a Faraday-equivalent chemical potential is introduced which allows chemical potential to be…
Under many conditions, biomolecules and nanoparticles associate by means of attractive bonds, due to hydrophobic attraction. Extracting the microscopic association or dissociation rates from experimental data is complicated by the…
We review the theoretical analyses and simulations of the interactions between curvature-inducing proteins and biomembranes. Laterally isotropic proteins induce spherical budding, whereas anisotropic proteins, such as Bin/Amphiphysin/Rvs…
Attosecond chemistry involves developing strategies to manipulate electronic coherent waves in molecules, which can influence the outcome of photoinduced reactions. While recent progress in this field calls for investigations of…
We present a structural data set of the 20 proteinogenic amino acids and their amino-methylated and acetylated (capped) dipeptides. Different protonation states of the backbone (uncharged and zwitterionic) were considered for the amino…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
As semiconductor technologies continue to scale down to the nanoscale, the efficient prediction of material properties becomes increasingly critical. The tight-binding (TB) method is a widely used semi-empirical approach that offers a…
The cytoskeleton in eukaryotic cells plays several crucial roles. In terms of intracellular transport, motor proteins use the cytoskeletal filaments as a backbone along which they can actively transport biological cargos such as vesicles…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
The local structure of a protein strongly impacts its function and interactions with other molecules. Therefore, a concise, informative representation of a local protein environment is essential for modeling and designing proteins and…
In organic proton-transfer ferroelectrics (OPTFe), molecules are linked together in a hydrogen-bonded network and proton transfer (PT) between molecules is the dominant mechanism of ferroelectric switching. Their fast switching frequencies…