Related papers: Ordering in a fibrinogen layer
Extrusion-based 3D printing is a widely utilized tool in tissue engineering, offering precise 3D control of bioinks to construct organ-sized biomaterial objects with hierarchically organized cellularized scaffolds. The internal organization…
In this study, the distributions of protein structure classes (or folding types) of experimentally determined structures from a legacy dataset and a comprehensive database (SCOP) are modeled precisely with geometric constructs such as…
The anisotropic structure of the myocardium is a key determinant of the cardiac function. To date, there is no imaging modality to assess in-vivo the cardiac fiber structure. We recently proposed Fibernet, a method for the automatic…
How can we design proteins with desired functions? We are motivated by a chemical intuition that both geometric structure and biochemical properties are critical to a protein's function. In this paper, we propose SurfPro, a new method to…
Computational analysis with the finite element method requires geometrically accurate meshes. It is well known that high-order meshes can accurately capture curved surfaces with fewer degrees of freedom in comparison to low-order meshes.…
In this paper, we will show that the recently introduced graphical model: Conditional Random Fields (CRF) provides a template to integrate micro-level information about biological entities into a mathematical model to understand their…
Using computer simulation, we have studied the random sequential adsorption of stiff linear $k$-mers onto a square lattice. Each such particle occupies $k$ adjacent lattice sites. During deposition, the two mutually perpendicular…
Entropy drives the phase behavior of colloids ranging from dense suspensions of hard spheres or rods to dilute suspensions of hard spheres and depletants. Entropic ordering of anisotropic shapes into complex crystals, liquid crystals, and…
In the context of elasticity theory, rigidity theorems allow to derive global properties of a deformation from local ones. This paper presents a new asymptotic version of rigidity, applicable to elastic bodies with sufficiently stiff…
The wetting properties of solid substrates with customary (i.e., macroscopic) random roughness are considered as a function of the microscopic contact angle of the wetting liquid and its partial pressure in the surrounding gas phase.…
Inferring the structural properties of a protein from its amino acid sequence is a challenging yet important problem in biology. Structures are not known for the vast majority of protein sequences, but structure is critical for…
Magnetic order and microwave absorption in amorphous ferromagnets and materials sintered from nanoscale ferromagnetic grains are investigated analytically and numerically within the random-anisotropy model. We show that a scaling argument…
This work presents a simple artificial neural network which classifies proteins into two classes from their sequences alone: the membrane protein class and the non-membrane protein class. This may be important in the functional assignment…
This work is concerned with the micro-architecture of multi-layer material that globally exhibits desired mechanical properties, for instance a negative apparent Poisson ratio. We use inverse homogenization, the level set method, and the…
Atomic force microscopy (AFM) with molecule-functionalized tips has emerged as the primary experimental technique for probing the atomic structure of organic molecules on surfaces. Most experiments have been limited to nearly planar…
Studying shape changing thick surfaces induced by differential growth helps us understand morphogenesis in biology and offers opportunities for device design. While ideal 2D differential growth maps have been well studied for both isotropic…
The short and intense pulses of the new X-ray free electron lasers, now operational or under construction, may make possible diffraction experiments on single molecule-sized objects with high resolution, before radiation damage destroys the…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
Resonance assignment is a critical first step in the investigation of protein structures using NMR spectroscopy. The development of assignment methods that require less experimental data is possible with prior knowledge of the…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…