Related papers: Rigidity analysis of HIV-1 protease
The protective capsid encasing the genetic material of Human Immunodeficiency Virus (HIV) has been shown to traverse the nuclear pore complex (NPC) intact, despite exceeding the passive diffusion threshold by over three orders of magnitude.…
When highly active antiretroviral therapy is administered for long periods of time to HIV-1 infected patients, most patients achieve viral loads that are ``undetectable'' by standard assay (i.e., HIV-1 RNA $ < 50$ copies/ml). Yet despite…
In this paper we analyze the vibrational spectra of a large ensemble of non-homologous protein structures by means of a novel tool, that we coin the Hierarchical Network Model (HNM). Our coarse-grained scheme accounts for the intrinsic…
Geometry of Liquid crystals as detectors of HIV twisted helical filaments is presented.
In this paper, we present a method to optimise rough set partition sizes, to which rule extraction is performed on HIV data. The genetic algorithm optimisation technique is used to determine the partition sizes of a rough set in order to…
Infection by many viruses begins with fusion of viral and cellular lipid membranes, followed by entry of viral contents into the target cell and ultimately, after many biochemical steps, integration of viral DNA into that of the host cell.…
This paper investigates the effect of drug treatment on the standard within-host HIV model, assuming that therapy occurs periodically. It is shown that eradication is possible under these periodic regimes, and we quantitatively characterize…
Recently, spin excitations in doped cuprates are measured using the resonant inelastic X-ray scattering (RIXS). The paramagnon dispersions show the large hardening effect in the electron-doped systems and seemingly doping-independence in…
HIV pre-exposure Prophylaxis (PrEP) has become essential for global HIV control, but its implementation coincides with rising bacterial STI rates among men who have sex with men (MSM). While risk-compensation behavioral changes like reduced…
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we show that an Ising model describing these interactions,…
Digital stiffness programmability is fulfilled with a heterogeneous mechanical metamaterial. The prototype consists of an elastomer matrix containing tessellations of diamond shaped cavities selectively confined with semi-rigid plastic beam…
We show that particle roughness leads to changes in the number, shape and resulting capillary force of liquid bridges in capillary suspensions. We created fluorescently labeled, raspberry-like particles with varying roughness by…
The paper considers a time-adaptive method for determination of drug efficacy in a parameter identification problem (PIP) for system of ordinary differential equations (ODE) which describe dynamics of the primary HIV infection. Optimization…
Adhesion hysteresis can be caused by elastic instabilities that are triggered by surface roughness or chemical heterogeneity. However, the role of these instabilities in adhesion hysteresis remains poorly understood because we lack…
We critically analyse the data available on the reduced cross-section in deeply inelastic $e p$ scattering from the H1 collaboration at HERA. We use available data on the longitudinal structure function to deduce the nature of $\d F_2/\d\ln…
Nanoindentation of viral capsids provides an efficient tool in order to probe their elastic properties. We investigate in the present work the various sources of stiffness heterogeneity as observed in Atomic Force Microscopy (AFM)…
We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of…
We theoretically explore the crystal structures of K$_x$picene, for which a new aromatic superconductivity has recently been discovered for $x=3$, by systematically performing first-principles full structural optimization covering the…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Heterochromatin protein 1 (HP1) participates in establishing and maintaining heterochromatin via its histone modification dependent chromatin interactions. In recent papers HP1 binding to nucleosomal arrays was measured in vitro and…