Related papers: Spike conformation transition in SARS-CoV-2 infect…
Temperature dependent high pressure electrical resistivity studies has been carried out on Ba(Fe_{1-x}Ru_{x})_{2}As_{2} single crystals with x = 0.12, 0.26 and 0.35, which correspond to under doped, optimally doped and over doped…
In temperate climates, infection rates of enveloped viruses peak during the winter. While these seasonal trends are established in influenza and human coronaviruses, the mechanisms driving the variation remain poorly understood and thus…
In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming…
Structure-based virtual screening aims to identify high-affinity ligands by estimating binding free energies between proteins and small molecules. However, the conformational flexibility of both proteins and ligands challenges conventional…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
The genomic ssRNA of coronaviruses is packaged within a helical nucleocapsid. Due to transitional symmetry of a helix, weakly specific cooperative interaction between ssRNA and nucleocapsid proteins leads to the natural selection of…
Significantly higher transmissibility of SARS CoV-2 (2019) compared to SARS CoV (2003) can be attributed to mutations of structural proteins (Spike S, Nucleocapsid N, Membrane M, and Envelope E) and the role played by non-structural…
A quantum theory on conformation-electron system is presented. Protein folding is regarded as the quantum transition between torsion states on polypeptide chain, and the folding rate is calculated by nonadiabatic operator method. The theory…
We have studied numerically the spectral correlations in a metallic phase and at the metal-insulator transition. We have calculated directly the two-point correlation function of the density of states $R(s,s')$. In the metallic phase, it is…
Predicting changes in binding free energy ($\Delta\Delta G$) is a vital task in protein engineering and protein-protein interaction (PPI) engineering for drug discovery. Previous works have observed a high correlation between $\Delta\Delta…
The Li$_2$S-P$_2$S$_5$ pseudo-binary system has been a valuable source of promising superionic conductors, with $\alpha$-Li$_3$PS$_4$, $\beta$-Li$_3$PS$_4$, HT-Li$_7$PS$_6$, and Li$_7$P$_3$S$_{11}$ having excellent room temperature Li-ion…
SARS-CoV-2 is an upper respiratory system RNA virus that has caused over 3 million deaths and infecting over 150 million worldwide as of May 2021. With thousands of strains sequenced to date, SARS-CoV-2 mutations pose significant challenges…
Structure fluctuations and conformational changes accompany all biological processes involving macromolecules. The paper presents a classification of protein residues based on the normalized equilibrium fluctuations of the residue centers…
Many types of neurons exhibit spike rate adaptation, mediated by intrinsic slow $\mathrm{K}^+$-currents, which effectively inhibit neuronal responses. How these adaptation currents change the relationship between in-vivo like fluctuating…
The COVID-19 pandemic has given rise to numerous articles from different scientific fields (epidemiology, virology, immunology, airflow physics...) without any effort to link these different insights. In this review, we aim to establish…
The COVID-19 pandemic has been a great catastrophe that upended human lives and caused millions of deaths all over the world. The rapid spread of the virus, with its early-stage exponential growth and subsequent 'waves', caught many medical…
Several important aspects related to SARS-CoV-2 transmission are not well known due to a lack of appropriate data. However, mathematical and computational tools can be used to extract part of this information from the available data, like…
We study the standard SIS model of epidemic spreading on networks where individuals have a fluctuating number of connections around a preferred degree $\kappa $. Using very simple rules for forming such preferred degree networks, we find…
A pipeline to evaluate the evolution of viral dynamics based on a new model-driven approach has been developed in the present study. The proposed methods exploit real data and the multiscale structure of the infection dynamics to provide…
We propose the conformon as a quantum of conformational change for energy transfer in alpha-helical proteins. The underlying mechanism of interaction between the quantum of excitation and the conformational degrees of freedom is nonlinear…