Related papers: Structural Stability and Immunogenicity of Peptide…
Many pairwise additive force fields are in active use for intrinsically disordered proteins (IDPs) and regions (IDRs), some of which modify energetic terms to improve description of IDPs/IDRs, but are largely in disagreement with solution…
In this paper we prove a stability result for inner fibrations in terms of the wide, or fat join operation on simplicial sets. We also prove some additional results on inner anodyne morphisms that may be of independent interest.
Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…
The behaviour and fate of tissue cells is controlled by the rigidity and geometry of their adhesive environment, possibly through forces localized to sites of adhesion. We introduce a mechanical model that predicts cellular force…
We describe a series of experiments involving the creation of cylindrical packings of star-shaped particles, and an exploration of the stability of these packings. The stars cover a broad range of arm sizes and frictional properties. We…
An exactly solvable model based on the topology of a protein native state is applied to identify bottlenecks and key-sites for the folding of HIV-1 Protease. The predicted sites are found to correlate well with clinical data on resistance…
mRNA technology has revolutionized vaccine development, protein replacement therapies, and cancer immunotherapies, offering rapid production and precise control over sequence and efficacy. However, the inherent instability of mRNA poses…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The network approach became a widely used tool to understand the behaviour of complex systems in the last decade. We start from a short description of structural rigidity theory. A detailed account on the combinatorial rigidity analysis of…
In contact-rich tasks, setting the stiffness of the control system is a critical factor in its performance. Although the setting range can be extended by making the stiffness matrix asymmetric, its stability has not been proven. This study…
Asymmetries and anisotropies are widespread in biological systems, including in the structure and dynamics of cilia and eukaryotic flagella. These microscopic, hair-like appendages exhibit asymmetric beating patterns that break…
Heterogeneous growth plays an important role in the shape and pattern formation of thin elastic structures ranging from the petals of blooming lilies to the cell walls of growing bacteria. Here we address the stability and regulation of…
For several decades, experimental and computational studies have been used to investigate the potential functional role of knots in protein structures. A property that has attracted considerable attention is thermal stability, i.e., the…
We investigate the effect of macromolecular crowding on protein folding, using purely repulsive crowding particles and a self-organizing polymer model of protein folding. We find that the thermodynamics of folding for typical alpha-, beta-…
The dynamical response of a lipid membrane to a local perturbation of its molecular symmetry is investigated theoretically. A density asymmetry between the two membrane leaflets is predominantly released by in-plane lipid diffusion or…
The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…
This work studies stability and robustness of a nonlinear system given as an interconnection of an ODE and a parabolic PDE subjected to external disturbances entering through the boundary conditions of the parabolic equation. To this end we…
Robustness of neural networks has recently attracted a great amount of interest. The many investigations in this area lack a precise common foundation of robustness concepts. Therefore, in this paper, we propose a rigorous and flexible…
This paper investigates the dynamics of immune response and autoimmunity with particular emphasis on the role of regulatory T cells (Tregs), T cells with different activation thresholds, and cytokines in mediating T cell activity. Analysis…
In a similar way in which the folding of single--domain proteins provide an important test in the study of self--organization, the folding of homodimers constitute a basic challenge in the quest for the mechanisms which are at the basis of…