Related papers: Rigidity analysis of HIV-1 protease
The consequences of recent experimental finding that hydrogen bonds of the anti-parallel $\beta $-sheet in nonspecific binding site of serine proteases become significantly shorter and stronger synchronously with the catalytic act are…
We prove results concerning the behavior of Hodge ideals under restriction to hypersurfaces or fibers of morphisms, and addition. The main tool is the description of restriction functors for mixed Hodge modules by means of the…
In contrast to previous belief, we provide examples of stationary ergodic random measures that are both hyperfluctuating and strongly rigid. Therefore, we study hyperplane intersection processes (HIPs) that are formed by the vertices of…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
Heparin has been found to have antiviral activity against SARS-CoV-2. Here, by means of sliding window docking, molecular dynamics simulations and biochemical assays, we investigate the binding mode of heparin to the virus spike…
Proteins are only moderately stable. It has long been debated whether this narrow range of stabilities is solely a result of neutral drift towards lower stability or purifying selection against excess stability is also at work - for which…
Rigid-body motions of protein secondary structure are often implicated in mecha-nisms of protein function. In GPCRs, evidence suggests that intracellular loop 2 (IL2) contains a segment characterized as a helix when the activated receptor…
We suggest that box shape trap enables to observe intrinsic properties of the repulsive Hubbard model in a fixed doping in contrast to the harmonic trap bringing about spatial variations of atom density profiles. In order to predict atomic…
Many proteins interact with and deform double-stranded DNA in cells. Single-molecule experiments have studied the elasticity of DNA with helix-deforming proteins, including proteins that bend DNA. These experiments increase the need for…
Epigenetic mechanisms of silencing via heritable chromatin modifications play a major role in gene regulation and cell fate specification. We consider a model of epigenetic chromatin silencing in budding yeast and study the bifurcation…
The rigid to floppy transitions and the associated intermediate phase in glasses are studied in the case where the local structure is not fully determined from the macroscopic concentration. The approach uses size increasing cluster…
The proteasome is a large biomolecular complex responsible for protein degradation. It is under intense research due to its fundamental role in cellular homeostasis, and tremendous potential for medicinal applications. Recent data from…
HERAFitter is an open-source package that provides a framework for the determination of the parton distribution functions (PDFs) of the proton and for many different kinds of analyses in Quantum Chromodynamics (QCD). It encodes results from…
We investigate one-dimensional harmonically trapped two-component systems for repulsive interaction strengths ranging from the non-interacting to the strongly interacting regime for Fermi-Fermi mixtures. A new and powerful mapping between…
We present a comprehensive study of the crystal structure of the thin-film, ferromagnetic topological insulator (Bi, Sb)$_{2-x}$V$_x$Te$_3$. The dissipationless quantum anomalous Hall edge states it manifests are of particular interest for…
A phenomenological model hamiltonian to describe the folding of a protein with any given sequence is proposed. The protein is thought of as a collection of pieces of helices; as a consequence its configuration space increases with the…
We consider frames in a finite-dimensional Hilbert space Hn where frames are exactly the spanning sets of the vector space. We present a method to determine the maximum robustness of a frame. We present results on tight subframes and…
This paper presents a motion analysis framework for an athlete wearing sport-specific flexible prosthesis based on the soft-rigid hybrid-link system. Such a motion analysis is a challenging problem because we need to consider the…
Training modern neural networks or models typically requires averaging over a sample of high-dimensional vectors. Poisoning attacks can skew or bias the average vectors used to train the model, forcing the model to learn specific patterns…
During primary HIV infection, the kinetics of plasma virus concentrations and CD4+ cell counts is very complex. Parametric and nonparametric models have been suggested for fitting repeated measurements of these markers. Alternatively,…