Related papers: Functionality and Protein-Water Interactions
The dynamics of quasicrystals is characterized by the existence of phason excitations in addition to the usual phonon modes. In order to investigate their interplay on an elementary level we resort to various one-dimensional model systems.…
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
We have shown recently that the notion of poking pairwise interactions along a chain provides a unifying framework for understanding the formation of both secondary and the tertiary protein structure based on symmetry and geometry.…
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…
In our recent works, based on the structural studies on water and interfacial water (topmost water layer at the solute/water interface), hydration free energy is derived and utilized to investigate the physical origin of hydrophobic…
Since the pioneering works of Pethig, Grant and Wuthrich on protein hydration layer, many studies have been devoted to find out if there are any general and universal characteristic features that can distinguish water molecules inside the…
Some natural proteins display recurrent structural patterns. Despite being highly similar at the tertiary structure level, repetitions within a single repeat protein can be extremely variable at the sequence level. We propose a mathematical…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
To comprehend the complexities of the ice-water interface, we perform a study that attempts to correlate the altered dynamics of water to its perturbed structure at, and due to, the interface. The deviation from bulk values of structural…
Velocity and density structure factors are measured over a hydrodynamic range of scales in a horizontal quasi-2d fluidized granular experiment, with packing fractions $\phi\in[10%,40%]$. The fluidization is realized by vertically vibrating…
We perform molecular dynamics simulations of 512 water-like molecules that interact via the TIP5P potential and are confined between two smooth hydrophobic plates that are separated by 1.10 nm. We find that the anomalous thermodynamic…
Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Predicting protein secondary structures such as alpha helices, beta sheets, and coils from amino acid sequences is essential for understanding protein function. This work presents a transformer-based model that applies attention mechanisms…
We study the kinetics of assembly of two plates of varying hydrophobicity, including cases where drying occurs and water strongly solvates the plate surfaces. The potential of mean force and molecular-scale hydrodynamics are computed from…
Compressing or cooling a fluid typically enhances its static interparticle correlations. However, there are notable exceptions. Isothermal compression can reduce the translational order of fluids that exhibit anomalous waterlike trends in…
In this article the configurational space of two simple protein models consisting of polymers composed of a periodic sequence of four different kinds of monomers is studied as a function of temperature. In the protein models, hydrogen bond…
Molecular dynamics simulations are used to study the occupancy and flow of water through nanotubes comprised of hydrophobic and hydrophilic atoms, which are arranged on a honeycomb lattice to mimic functionalized carbon nanotubes (CNTs). We…
With the aim to study the relationship between protein sequences and their native structures, we adopt vectorial representations for both sequence and structure. The structural representation is based on the Principal Eigenvector of the…
Ion hydration and interfacial water play crucial roles in numerous phenomena ranging from biological to industrial systems. Although biologically relevant (and mostly smaller) ions have been studied extensively in this context, very little…