Related papers: Deciphering general characteristics of residues co…
Deep neural networks with short residual connections have demonstrated remarkable success across domains, but increasing depth often introduces computational redundancy without corresponding improvements in representation quality. We…
Signal transmission at the molecular level in many biological complexes occurs through allosteric transitions. They describe the response a complex to binding of ligands at sites that are spatially well separated from the binding region. We…
Aggregation of amphiphiles through the action of hydrophobic interactions is a common feature in soft condensed matter systems and is of particular importance in the context of biophysics as it underlies both the generation of functional…
Short polymer chains exhibit clear deviations from Gaussian end-to-end distance statistics, yet the molecular mechanism by which Gaussian behavior is recovered in long chains remains unestablished. Atomistic molecular dynamics simulations…
Predicting protein structure from the amino acid sequence has been a challenge with theoretical and practical significance in biophysics. Despite the recent progresses elicited by improved residue-residue contact prediction, contact-based…
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
A dissipative stochastic sandpile model is constructed and studied on small world networks in one and two dimensions with different shortcut densities $\phi$, where $\phi=0$ represents regular lattice and $\phi=1$ represents random network.…
Applying multicanonical simulations we investigated folding properties of off-lattice heteropolymers employing a mesoscopic hydrophobic-polar model. We study for various sequences folding channels in the free-energy landscape by comparing…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
Adaptive transport networks in biological and physical systems exhibit hierarchical organization, characteristic channel spacing, and robust scaling relations. Existing adaptive network models, formulated on a lattice, successfully…
In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a…
Based on nonlinear prediction and information theory, vertical heterogeneity of predictability and information loss rate was obtained over the Northern Hemisphere. In seasonal to interannual time scales, the predictability is low in lower…
Many signalling functions in molecular biology require proteins bind to substrates such as DNA in response to environmental signals such as the simultaneous binding to a small molecule. Examples are repressor proteins which may transmit…
Recent research in both the experimental and mathematical communities has focused on biochemical interaction systems that satisfy an "absolute concentration robustness" (ACR) property. The ACR property was first discovered experimentally…
Pairs of similar compounds that only differ by a small structural modification but exhibit a large difference in their binding affinity for a given target are known as activity cliffs (ACs). It has been hypothesised that quantitative…
Ambient noise tomography relies on the assumption that the seismic wavefield is equipartitioned. In practice, ambient noise sources are spatially and temporally heterogeneous, producing biased estimates of the Green's function between…
The changes in the local and global dynamics of azide-labelled Lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N$_3$ to alanine…
We employed the random graph theory approach to analyze the protein-protein interaction database DIP (Feb. 2004), for seven species (S. cerevisiae, H. pylori, E. coli, C. elegans, H. sapiens, M. musculus and D. melanogaster). Several global…
Deep Residual Networks present a premium in performance in comparison to conventional networks of the same depth and are trainable at extreme depths. It has recently been shown that Residual Networks behave like ensembles of relatively…
A protein residue network (PRN) is a network of interacting amino acids within a protein. We describe characteristics of a sparser, highly central and more volatile sub-network of a PRN called the short-cut network (SCN), as a protein folds…