Related papers: Efficient fold-change detection based on protein-p…
Eukaryotic adaptation pathways operate within wide-ranging environmental conditions without stimulus saturation. Despite numerous differences in the adaptation mechanisms employed by bacteria and eukaryotes, all require energy consumption.…
Typical contact detection is based on the monitoring of a threshold value in the force and torque signals. The selection of a threshold is challenging for robots operating in unstructured or highly dynamic environments, such in a household…
Optical molecular sensing techniques are often limited by the refractive index change associated with the probed interactions. In this work, we present a closed form analytical model to estimate the magnitude of optical refractive index…
Interactions between proteins are hard to decipher. Protein-protein interactions are difficult problem to address because they are not based on differences in charge type like protein-DNA or protein-lipid interactions. In this manuscript we…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
Light-matter interaction dynamics is governed by the strength of local coupling constants, tailored by surrounding electromagnetic structures. Characteristic decay times in dipole-allowed fluorescent transitions are much faster than…
The mechanical model based on beads and springs, which we recently proposed to study non-specific DNA-protein interactions [J. Chem. Phys. 130, 015103 (2009)], was improved by describing proteins as sets of interconnected beads instead of…
In this letter, a novel method for change detection is proposed using neighborhood structure correlation. Because structure features are insensitive to the intensity differences between bi-temporal images, we perform the correlation…
We present a statistical approach to protein structure by introducing a representation of protein folds based on simple observables defined as frequencies of oriented cycles in contact graphs. Motivated by the idea that these cycles may…
Equilibrium and out-of-equilibrium transitions of an off-lattice protein model have been identified and studied. In particular, the out-of-equilibrium dynamics of the protein undergoing mechanical unfolding is investigated, and by using a…
The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…
We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Unsupervised transfer learning-based change detection methods exploit the feature extraction capability of pre-trained networks to distinguish changed pixels from the unchanged ones. However, their performance may vary significantly…
Despite recent advances in protein-ligand structure prediction, deep learning methods remain limited in their ability to accurately predict binding affinities, particularly for novel protein targets dissimilar from the training set. In…
Protein-protein interactions are fundamental to many biological processes. Experimental screens have identified tens of thousands of interactions and structural biology has provided detailed functional insight for select 3D protein…
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…
A new general algorithm for optimization of potential functions for protein folding is introduced. It is based upon gradient optimization of the thermodynamic stability of native folds of a training set of proteins with known structure. The…
Transcriptional regulatory network inference methods have been studied for years. Most of them relie on complex mathematical and algorithmic concepts, making them hard to adapt, re-implement or integrate with other methods. To address this…