Related papers: Rigidity analysis of HIV-1 protease
We numerically investigate the effects of fiber aspect ratio, roughness, flexibility, and flow inertia on the rheology of concentrated suspensions. We perform direct numerical simulations modeling the fibers, suspended in an incompressible…
Methods are lacking to handle the problem of survival analysis in the presence of an interval-censored covariate, specifically the case in which the conditional hazard of the primary event of interest depends on the occurrence of a…
Type 1 fimbriae mediate adhesion of uropathogenic Escherichia coli (UPEC) to host cells. It has been hypothesized that fimbriae can, by their ability to uncoil under exposure to force, reduce fluid shear stress on the adhesin-receptor…
Incidence estimation of HIV infection can be performed using recent infection testing algorithm (RITA) results from a cross-sectional sample. This allows practitioners to understand population trends in the HIV epidemic without having to…
We present experimental measurements of the cholesteric-smectic phase transition of suspensions of charged semiflexible rods as a function of rod flexibility and surface charge. The rod particles consist of the bacteriophage M13 and closely…
Chronic infections of the human immunodeficiency virus (HIV) create a very complex co-evolutionary process, where the virus tries to escape the continuously adapting host immune system. Quantitative details of this process are largely…
We study the non-monotonic force-extension behaviour of helical ribbons using a new model for inextensible elastic strips. Unlike previous rod models our model predicts hysteresis behaviour for low-pitch ribbons of arbitrary material…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Starting from the lead structure we have identified in our previous works, we are extending our insight understanding of its potential inhibitory effect against both EGFR and HER2 receptors. Herein and using extended molecular dynamic…
We have extended our experimentally constrained molecular relaxation technique (P. Biswas {\it et al}, Phys. Rev. B {\bf 71} 54204 (2005)) to hydrogenated amorphous silicon: a 540-atom model with 7.4 % hydrogen and a 611-atom model with 22…
Protein electrostatics have been demonstrated to play a vital role in protein functionality, with many functionally important amino acid residues exhibiting an electrostatic state that is altered from that of a normal amino acid residue.…
Multiple mechanisms in the HIV lifecycle play a role in its ability to evade therapy and become a chronic, difficult-to-treat infection. Within its major cellular target, the activated T cell, many steps occur between viral entry and viral…
Conventional drugs work, as a rule, by inhibiting the enzymatic activity of specific proteins, capping their active site. In this paper we present a model of non- conventional drug design based on the inhibiting effects small peptides…
In this paper, we construct a model to describe the transmission of HIV in a homogeneous host population. By considering the specific mechanism of HIV, we derive a model structured in three successive stages: (i) primary infection, (ii)…
Crystallographic data comes from a space-time average over all the unit cells within the crystal, so dynamic phenomena do not contribute significantly to the diffraction data. Many efforts have been made to reconstitute the movement of the…
We point out that although a litany of studies have been published on atoms in hard-wall confinement, they have not been systematic or have not used robust numerical methods. We report a methodical study of atoms in hard-wall confinement…
Protein-protein interactions (protein functionalities) are mediated by water, which compacts individual proteins and promotes close and temporarily stable large-area protein-protein interfaces. In their classic paper Kyte and Doolittle (KD)…
The problem of inferring proteins from complex peptide cocktails (digestion products of biological samples) in shotgun proteomic workflow sets extreme demands on computational resources in respect of the required very high processing…
The government's effort to alleviate HIV stigma has been justified by the suppression effect of stigma on the HIV testing rate. Nevertheless, the deterrence effect of stigma on undesirable sexual behaviours has long been overlooked. This…
A significant range of geometric structures whose rigidity is explored for both practical and theoretical purposes are formed by modifying generically isostatic triangulated spheres. In the block and hole structures (P, p), some edges are…