Related papers: Fine structures of Intrinsically Disordered Protei…
A hierarchical (triple scale) simulation methodology is presented for the prediction of the dynamical and rheological properties of high molecular weight entangled polymer melts. The methodology consists of atomistic, moderately…
Although machine learning has transformed protein structure prediction of folded protein ground states with remarkable accuracy, intrinsically disordered proteins and regions (IDPs/IDRs) are defined by diverse and dynamical structural…
Although both RNA and proteins have densely packed native structures, chain organizations of these two biopolymers are fundamentally different. Motivated by the recent discoveries in chromatin folding that interphase chromosomes have…
While deep learning has revolutionized the prediction of rigid protein structures, modelling the conformational ensembles of Intrinsically Disordered Proteins (IDPs) remains a key frontier. Current AI paradigms present a trade-off: Protein…
We propose the first, to our knowledge, coarse-grained modeling strategy for peptides where the effect of changes of the pH can be efficiently described. The idea is based on modeling the effects of the pH value on the main driving…
Modelling micro- and meso-scopic scale thermodynamic and transport properties of soft condensed matter hinges upon its representation. This is especially relevant for polar solvents such as water, since these require effective…
The study of protein interactions has generated great interest in the food industry. Therefore, research on new supramolecular structures shows promise. Supramolecular structures of the whey proteins {\alpha}-lactalbumin and…
From bird flocks and fish schools to migrating cell sheets, collective motion is a ubiquitous biological phenomenon that inspires quantitative modeling through self-propelled particle (SPP) frameworks. Conventional SPP models prescribe…
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep…
Protein-protein interactions (PPIs) are fundamental to numerous cellular processes, and their characterization is vital for understanding disease mechanisms and guiding drug discovery. While protein language models (PLMs) have demonstrated…
The concepts of globule and random coil were developed to describe the phases of homopolymers and then used to characterize the denatured state of structured cytosolic proteins and intrinsically disordered proteins. Using multi-scale…
A popular concept which describes the structure of polymer interfaces by ``intrinsic profiles'' centered around a two dimensional surface, the ``local interface position'', is tested by extensive Monte Carlo simulations of interfaces…
The paper uses the spring potential to present interaction between the coarse-grained interfacial particles of the $\alpha$-Al2O3/$\alpha$-Al2O3 and $\alpha$-Fe2O3/$\alpha$-Fe2O3 contacts in the sliding friction study of these micron-scale…
The fine structure of the isoscalar giant quadrupole resonance in ^{208}Pb, observed in high-resolution (p,p') and (e,e') experiments, is studied using the entropy index method. In a novel way, it enables to determine the number of scales…
The knowledge of the binding energy of molecules on astrophysically relevant ices can help to obtain an estimate of the desorption rate, i.e. the molecules residence time on the surface. This represents an important parameter for…
Iron phosphate glasses (IPG) have been proposed as futuristic glass material for nuclear waste immobilization, anode material for lithium batteries and also as bioactive glass. In the last decade, there have been attempts to propose…
After the recent ground-breaking advances in protein structure prediction, one of the remaining challenges in protein machine learning is to reliably predict distributions of structural states. Parametric models of fluctuations are…
Protein-Protein Interactions (PPIs) are fundamental in various biological processes and play a key role in life activities. The growing demand and cost of experimental PPI assays require computational methods for efficient PPI prediction.…
The relationship between interactions, flexibility and disorder in proteins has been explored from many angles: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…