Related papers: Rigidity analysis of HIV-1 protease
We study the elastic response of rigid, wire frame particles in concentrated, glassy suspensions to a step strain by applying the simple, geometric methods developed in part I. The wire frame particles are comprised of thin, rigid rods of…
HIV/AIDs Regimen specification one of many problems for which bioinformaticians have implemented and trained machine learning methods such as neural networks. Predicting HIV resistance would be much easier, but unfortunately we rarely have…
The paper presents a systematic approach for stiffness modeling of manipulators with complex and hybrid structures using matrix structural analysis. In contrast to previous results, it is suitable for mixed architectures containing…
We have performed x-ray absorption spectroscopy (XAS) and x-ray photoemission spectroscopy (XPS) studies of single crystal Ba_{1-x}K_{x}BiO_{3} (BKBO) covering the whole composition range $0 \leq x \leq 0.60$. Several features in the oxygen…
Social context plays an important role in perpetuating or reducing HIV risk behaviors. This study analyzed the network and individual attributes that were associated with the likelihood that people who inject drugs (PWID) will engage in HIV…
HIV dynamical models are often based on non-linear systems of ordinary differential equations (ODE), which do not have analytical solution. Introducing random effects in such models leads to very challenging non-linear mixed-effects models.…
To overcome antimalarial drug resistance, carbohydrate derivatives as selective PfHT1 inhibitor have been suggested in recent experimental work with orthosteric and allosteric dual binding pockets. Inspired by this promising therapeutic…
This is a summary of mathematical tools we used in research of analyzing the structure of proteins with amyloid form \cite{xi2024Top}. We defined several geometry indicators on the discrete curve namely the hop distance, the discrete…
Results from the HERA experiments, H1 and ZEUS, on $e^\pm p$ deep inelastic scattering (DIS) provide an important contribution to the knowledge of the proton structure and QCD. The data were collected in the years 1994-2000 (HERA I) and…
The evolutionary dynamics of HIV during the chronic phase of infection is driven by the host immune response and by selective pressures exerted through drug treatment. To understand and model the evolution of HIV quantitatively, the…
In this study, we investigated the inhibition of SARS-CoV-2 spike glycoprotein with HIV drugs and their combinations. This glycoprotein is essential for the reproduction of the SARS-COV-2 virus, so its inhibition opens new avenues for the…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
We study within-host HIV dynamics using a three--component nonlinear ordinary differential equation model for healthy CD4$^{+}$ T cells, infected CD4$^{+}$ T cells, and free virus. In addition to the baseline model without treatment, we…
The Bean-Livingston barrier at the interface of type-II superconductor/soft-magnet heterostructures is studied on the basis of the classical London approach. This shows a characteristic dependence on the geometry of the particular structure…
The structure of the Baxter adhesive hard sphere fluid is examined using computer simulation. The radial distribution function (which exhibits unusual discontinuities due to the particle adhesion) and static structure factor are calculated…
When investigating the mode of hydrogen activation by [Fe] hydrogenases, not only the chemical reactivity at the active site is of importance but also the large-scale conformational change between the so-called open and closed…
Human immunodeficiency virus (HIV) capsid proteins spontaneously assemble around the genome into a protective protein shell called the capsid, which can take on a variety of shapes broadly classified as conical, cylindrical and irregular.…
We combine experiments with simulations to investigate the fluid-structure interaction of a flexible helical rod rotating in a viscous fluid, under low Reynolds number conditions. Our analysis takes into account the coupling between the…
The scalability of spin qubit devices is conditioned by qubit-to-qubit variability. Disorder in the host materials indeed affects the wave functions of the confined carriers, which leads to variations in their charge and spin properties.…
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Knowing the virus' fitness as a function of its proteomic…