Related papers: Kinetics of seeded protein aggregation: theory and…
In a shotgun proteomics experiment, proteins are the most biologically meaningful output. The success of proteomics studies depends on the ability to accurately and efficiently identify proteins. Many methods have been proposed to…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…
In the abstract Tile Assembly Model (aTAM) square tiles self-assemble, autonomously binding via glues on their edges, to form structures. Algorithmic aTAM systems can be designed in which the patterns of tile attachments are forced to…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
We investigate vapor homogeneous nucleation in a superheated Lennard Jones liquid with computer simulations. Special simulation techniques are required to address this study since the nucleation of a critical vapor bubble --one that has…
Proteins employ the information stored in the genetic code and translated into their sequences to carry out well-defined functions in the cellular environment. The possibility to encode for such functions is controlled by the balance…
Protein molecules often self-assemble by means of non-covalent physical bonds to form extended filaments, such as amyloids, F-actin, intermediate filaments, and many others. The kinetics of filament growth is limited by the disassembly…
We present several numerical results on granular mixtures. In particular, we examine the efficiency of diffusion as a mixing mechanism in these systems. The collisions are inelastic and to compensate the energy loss, we thermalize the…
Proteins are biomolecules of life. They fold into a great variety of three-dimensional (3D) shapes. Underlying these folding patterns are many recurrent structural fragments or building blocks (analogous to `LEGO bricks'). This paper…
For the purpose of propagating information and ideas through a social network, a seeding strategy aims to find a small set of seed users that are able to maximize the spread of the influence, which is termed as influence maximization…
A method that reconstructs protein residue networks using suitable node selection and edge recovery policies produced numerical observations that correlate strongly (Pearson's correlation coefficient < -0.83) with published folding rates…
In this work we study the stochastic process of two-species coagulation. This process consists in the aggregation dynamics taking place in a ring. Particles and clusters of particles are set in this ring and they can move either clockwise…
Graph matching aims to find the latent vertex correspondence between two edge-correlated graphs and has found numerous applications across different fields. In this paper, we study a seeded graph matching problem, which assumes that a set…
We present a parallelized bijective graph matching algorithm that leverages seeds and is designed to match very large graphs. Our algorithm combines spectral graph embedding with existing state-of-the-art seeded graph matching procedures.…
Using exhaustive Monte Carlo simulations we study the kinetics and mechanism of fibril formation using lattice models as a function of temperature and the number of chains. While these models are, at best, caricatures of peptides, we show…
Super-resolution imaging techniques have largely improved our capabilities to visualize nanometric structures in biological systems. Their application further enables one to potentially quantitate relevant parameters to determine the…
Protein assembly plays an important role throughout all phyla of life, both physiologically and pathologically. In particular, aggregation and polymerization of proteins are key-strategies that regulate cellular function. In recent years,…
Atomic-scale simulations are performed to study the effect of solute segregation on the shear-induced motion of select grain boundaries in the classical $\alpha$-Fe/C system. At shear rates larger than the solute diffusion rate, we observe…
In this paper, a new information theoretic framework for graph matching is introduced. Using this framework, the graph isomorphism and seeded graph matching problems are studied. The maximum degree algorithm for graph isomorphism is…