Related papers: Deciphering general characteristics of residues co…
The ABC (ATP Binding Cassette) transporter protein superfamily comprises a large number of ubiquitous and functionally versatile proteins conserved from archaea to humans. ABC transporters have a key role in many human diseases and also in…
Fossil DNA preservation varies with depositional environments and diagenesis, producing fragments of heterogeneous origins and degradation states. We use first-principles biomolecular analysis to classify fossil molecular environments into…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
The thermodynamic behavior of a three-dimensional off-lattice model for protein folding is probed. The model has only two types of residues, hydrophobic and hydrophilic. In absence of local interactions, native structure formation does not…
We construct a one-bead-per-residue coarse-grained dynamical model to describe intrinsically disordered proteins at significantly longer timescales than in the all-atom models. In this model, inter-residue contacts form and disappear during…
Physicochemical characterization of materials is central to the field of science and engineering and is essential to design new/engineered materials with specific properties. Assays available for small-molecules, e.g., XRD, NMR, LC-MS,…
In this work we propose a novel interpretation of residual networks showing that they can be seen as a collection of many paths of differing length. Moreover, residual networks seem to enable very deep networks by leveraging only the short…
What makes a network complex, in addition to its size, is the interconnected interactions between elements, disruption of which inevitably results in dysfunction. Likewise, the brain networks' complexity arises from interactions beyond pair…
Identifying and removing microplastics (MPs) from the environment is a global challenge. This study explores how the colloidal fraction of common MPs behave at aqueous interfaces of liquid crystal (LC) films. We observed polyethylene (PE)…
The structure of egocentric networks reflects the way people balance their need for strong, emotionally intense relationships and a diversity of weaker ties. Egocentric network structure can be quantified with 'social signatures', which…
The connectivity pattern of networks, which are based on a correlation between ground level temperature time series, shows a dominant dense stripe of links in the southern ocean. We show that statistical categorization of these links yields…
Spatial organization of proteins in cells is important for many biological functions. In general, the nonlinear, spatially coupled models for protein-pattern formation are only accessible to numerical simulations, which has limited insight…
What characterises a solid is its way to respond to external stresses. Ordered solids, such crystals, display an elastic regime followed by a plastic one, both well understood microscopically in terms of lattice distortion and dislocations.…
The $\alpha$ and $\beta$ subunits comprising the hexameric assembly of F1-ATPase share a high degree of structural identity, though low primary identity. Each subunit binds nucleotide in similar pockets, yet only $\beta$ subunits are…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
We predicted residual fluid intelligence scores from T1-weighted MRI data available as part of the ABCD NP Challenge 2019, using morphological similarity of grey-matter regions across the cortex. Individual structural covariance networks…
How typical elements that shape organisms, such as protein secondary structures, have evolved, or how evolutionarily susceptible/resistant they are to environmental changes, are significant issues in evolutionary biology, structural…
The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…
Many experiments have shown that the conductance histograms of metallic atomic-sized contacts exhibit a peak structure, which is characteristic of the corresponding material. The origin of these peaks still remains as an open problem. In…
Core-periphery is a key feature of large-scale networks underlying a wide range of social, biological, and transportation phenomena. Despite its prevalence in empirical data, it is unclear whether this property is a consequence of more…