Related papers: Spike conformation transition in SARS-CoV-2 infect…
Self-adaptive dynamics occurs in many physical systems such as socio-economics, neuroscience, or biophysics. We formalize a self-adaptive modeling approach, where adaptation takes place within a set of strategies based on the history of the…
In this work, we aim to study that the dynamics behavior for cumulative number of SARS-CoV-2 pandemic can provide information on the overall behavior of the spread over daily time.The cumulative data can be synthesized in an empirical form…
Zhou et al. reported the discovery of RmYN02, a strain closely related to SARS-CoV-2, which is claimed to contain a natural PAA amino acid insertion at the S1/S2 junction of the spike protein at the same position of the PRRA insertion that…
Proteins play a key role in facilitating the infectiousness of the 2019 novel coronavirus. A specific spike protein enables this virus to bind to human cells, and a thorough understanding of its 3-dimensional structure is therefore critical…
The objective of this paper is to provide a mathematical model to construct a barrier that may be useful to prevent the penetration of different viruses (Eg. SARS-COV-2) as well as charged aerosols through the concept of electrostatic…
Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing…
The resistivity around the ferromagnetic transition temperature in the double exchange model is studied by the Schwinger boson approach. The spatial spin correlation responsible for scattering of conduction electrons are taken into account…
A previously established multiscale population genetics model states that fitness can be inferred from the physical properties of proteins under the physiological assumption that a loss of stability by any protein confers the lethal…
A central question is how the conformational changes of proteins affect their function and the inhibition of this function by drug molecules. Many enzymes change from an open to a closed conformation upon binding of substrate or inhibitor…
Two phenomena have been recently observed in high-mobility Si MOS structures: (1) strong enhancement of the metallic conduction at low temperatures, T < 2K, and (2) the scaling behavior of the temperature and electric field dependences of…
In December 2019, a newly discovered SARS-CoV-2 virus was emerged from China and propagated worldwide as a pandemic. In the absence of preventive medicine or a ready to use vaccine, mathematical models can provide useful scientific insights…
Consider a migration process based on a closed network of N stations with K_N customers. Each station is a ./M/\infty queue with service (migration) rate mu. Upon departure, a customer is routed at random to another station. In addition to…
We study a bi-virus susceptible-infected-susceptible (SIS) epidemic model in which individuals are either susceptible or infected with one of two virus strains, and consider mutation-driven transitions between strains. The general case of…
Influenza virus evolves to escape from immune system antibodies that bind to it. We used free energy calculations with Einstein crystals as reference states to calculate the difference of antibody binding free energy ($\Delta\Delta G$)…
We propose a realistic model for the evolution of the COVID-19 pandemic subject to the lockdown and quarantine measures, which takes into account the time-delay for recovery or death processes. The dynamic equations for the entire process…
Spike proteins, 1200 amino acids, are divided into two nearly equal parts, S1 and S2. We review here phase transition theory, implemented quantitatively by thermodynamic scaling. The theory explains the evolution of Coronavirus extremely…
We study spin-$S$ Ising models with $p$-spin interactions on the one-dimensional chain and the two-dimensional square lattice. Here, $S$ denotes the magnitude of the spin and $p$ represents the number of spins involved in each interaction.…
In many biological applications, we would like to be able to computationally predict mutational effects on affinity in protein-protein interactions. However, many commonly used methods to predict these effects perform poorly in important…
The electronic structures of Sn and Pb implanted SiO2 are studied using soft X-ray absorption (XAS) and emission (XES) spectroscopy. We show, using reference compounds and ab initio calculations, that the presence of Pb-O and Sn-O…
Conformational changes upon protein-protein association are the key element of the binding mechanism. The study presents a systematic large-scale analysis of such conformational changes in the side chains. The results indicate that short…