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A theory is set up of spherical proteins interacting by screened electrostatics and constant adhesion, in which the effective adhesion parameter is optimized by a variational principle for the free energy. An analytical approach to the…
Distribution shifts between training and testing datasets significantly impair the model performance on graph learning. A commonly-taken causal view in graph invariant learning suggests that stable predictive features of graphs are causally…
This paper presents a stability test for a class of interconnected nonlinear systems motivated by biochemical reaction networks. One of the main results determines global asymptotic stability of the network from the diagonal stability of a…
Mutations in proteins can have deleterious effects on a protein's stability and function, which ultimately causes particular diseases. Genetically inherited muscular dystrophies (MDs) include several genetic diseases, which cause increasing…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
The native conformation of structured proteins is stabilized by a complex network of interactions. We analyzed the elementary patterns that constitute such network and ranked them according to their importance in shaping protein sequence…
Atomic displacements of hydrated proteins are dominated by phonon vibrations at low temperatures and by dissipative large-amplitude motions at high temperatures. A crossover between the two regimes is known as a dynamical transition. Recent…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
Protein structures are much more conserved than sequences during evolution. Based on this observation, we investigate the consequences of structural conservation on protein evolution. We study seven of the most studied protein folds,…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
The increase of aqueous solubility of nonpolar compounds upon cooling and the cold denaturation of proteins are established experimental facts. Both phenomena have been hypothesized to be related to restructuring of the hydrogen bond…
Through modelling and simulations we show that material instabilities play a dominant role in the mechanical behavior of the fibrous collagen Extracellular Matrix (ECM), as observed when the ECM is deformed by contractile biological cells.…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
For cyclic heat engines operating in a finite cycle period, thermodynamic quantities have intercycle and intracycle correlations. By tuning the driving protocol appropriately, we can get the negative intercycle correlation to reduce the…
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…
It is shown how the combination of atomic deposition and nonlinear diffusion may lead, below a critical temperature, to the growth of nonuniform layers on a substrate. The dynamics of such a system is of the Cahn-Hilliard type, supplemented…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
Protein-based high internal phase emulsions (HIPEs) have gained tremendous attention in diverse fields, but their mechanism in the emulsification process remains elusive. In this article, HIPEs were stabilized directly by food-grade…
Using the theory of elasticity of polymer gels we show that large-scale cross-link density patterns written into the structure of the network in the melt state, can be revealed upon swelling by monitoring the monomer density patterns. We…
Active gels made of cytoskeletal proteins are valuable materials with attractive non-equilibrium properties such as spatial self-organization and self-propulsion. At least four typical routes to spatial patterning have been reported to date…