Related papers: Ordering in a fibrinogen layer
The loading of a granular material induces anisotropies of the particle arrangement (fabric) and of the material's strength, incremental stiffness, and permeability. Thirteen measures of fabric anisotropy are developed, which are arranged…
Proteins are fundamental biological entities mediating key roles in cellular function and disease. This paper introduces a multi-scale graph construction of a protein -- HoloProt -- connecting surface to structure and sequence. The surface…
We introduce a minimal model of solid-forming anisotropic molecules that displays, in thermal equilibrium, surface orientational order without bulk orientational order. The model reproduces the nonequilibrium behavior of recent experiments…
This review is a tutorial for scientists interested in the problem of protein structure prediction, particularly those interested in using coarse-grained molecular dynamics models that are optimized using lessons learned from the energy…
Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the…
We introduce a generative model for protein backbone design utilizing geometric products and higher order message passing. In particular, we propose Clifford Frame Attention (CFA), an extension of the invariant point attention (IPA)…
When nanoparticles (NPs) are introduced into a biological solution, layers of biomolecules form on their surface, creating a corona. Understanding how the structure of the protein evolves into the corona is essential for evaluating the…
The measurement of in-plane birefringence ($\Delta{n}$) of ultrathin film is challenging due to a significant deviation of physical properties of materials in ultrathin regime as compared to that in bulk state. Surface plasmon resonance…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
We present the effect of different stacking orders on carrier transport properties of multi-layer black phosphorous. We consider three different stacking orders AAA, ABA and ACA, with increasing number of layers (from 2 to 6 layers). We…
In many growth processes particles are highly mobile in an active layer at the surface, but are relatively immobile once incorporated in the bulk. We study models in which atoms are allowed to interact, equilibrate, and order on the…
The dynamics of cellular pattern formation is crucial for understanding embryonic development and tissue morphogenesis. Recent studies have shown that human dermal fibroblasts cultured on liquid crystal elastomers can exhibit an increase in…
We study the atomic oxygen adsorption on Pb(111) surface by using density-functional theory within the generalized gradient approximation and a supercell approach. The atomic and energetic properties of purely on-surface and subsurface…
In this work, we present a variant of the multilayer random sequential adsorption (RSA) process that is inspired by orthogonal resource sharing in wireless communication networks. In the one-dimensional (1D) version of this variant, the…
A collection of thin structures buckle, bend, and bump into each-other when confined. This contact can lead to the formation of patterns: hair will self-organize in curls; DNA strands will layer into cell nuclei; paper, when crumpled, will…
Under the most common experimental conditions, the adsorption of proteins to solid surfaces is an spontaneous process that leads to a rather compact layer of randomly oriented molecules. Due to the importance of this process for the…
The rheological properties of fibrin networks have been of long-standing interest. As such there is a wealth of studies of their shear and tensile responses, but their compressive behavior remains unexplored. Here, by characterization of…
The adsorption of atomic oxygen and its inclusion into subsurface sites on Ag(210) and Ag(410) surfaces have been investigated using density functional theory. We find that--in the absence of adatoms on the first metal layer--subsurface…
The local fiber orientation is a micro-structural feature crucial for the mechanical properties of parts made from fiber reinforced polymers. It can be determined from micro-computed tomography data and subsequent quantitative analysis of…
It has been a long-standing materials science challenge to establish structure-property relations in amorphous solids. Here we introduce a rotation-variant local structure representation that enables different predictions for different…