相关论文: Protein-Polymer Mixtures in the Colloid Limit: Agg…
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…
Proteins are linear chain molecules that play a central role in life and health. Protein native state folds are modular assemblies of space-filling building blocks of {\alpha}-helices, \{beta}-sheets and tight turns. Here we deduce the…
Asymmetric patchy particle models have recently been shown to describe the crystallization of small globular proteins with near quantitative accuracy. Here, we investigate how asymmetry in patch geometry and bond energy generally impact the…
Phase separations in strongly coupled fine particles in plasmas are discussed and two-component mixtures are simulated by molecular dynamics with the background plasma being treated as continuum. The system size of laboratory experiments is…
Inelastic collisions occur among regolith particles, such as those in the ejecta curtain from a crater, and may cause clustering or agglomeration of particles and thus produce discrete patterns of ejecta deposits around a crater. Previous…
We propose an algorithmic strategy for improving the efficiency of Monte Carlo searches for the low-energy states of proteins. Our strategy is motivated by a model of how proteins alter their shapes. In our model when proteins fold under…
The phase-separation occurring in a system of mutually interacting proteins that can bind on specific sites of a chromatin fiber is here investigated. This is achieved by means of extensive Molecular Dynamics simulations of a simple polymer…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
The paper investigates a novel approach, based on Constraint Logic Programming (CLP), to predict the 3D conformation of a protein via fragments assembly. The fragments are extracted by a preprocessor-also developed for this work- from a…
Micrometre sized colloidal particles can be viewed as large atoms with tailorable size, shape and interactions. These building blocks can assemble into extremely rich structures and phases, in which the thermal motions of particles can be…
We formulate and characterize a model to describe the dynamics of semiflexible polymers in the presence of activity due to motor proteins attached irreversibly to a substrate, and a transverse pulling force acting on one end of the…
We present a computational study on the folding and aggregation of proteins in aqueous environment, as function of its concentration. We show how the increase of the concentration of individual protein species can induce a partial unfolding…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
Nanoparticle (NP)-protein complexes exhibit the correct identity of NP in biological media. Therefore, protein-NP interactions should be closely explored to understand and to modulate the nature of NPs in medical implementations. This…
This paper analyzes the compaction behavior of assemblies composed of soft (elastic) spherical particles beyond the jammed state, using three-dimensional non-smooth contact dynamic simulations. The assemblies of particles are characterized…
We consider a model of an extensible semiflexible filament moving in two dimensions on a motility assay of motor proteins represented explicitly as active harmonic linkers. Their heads bind stochastically to polymer segments within a…
We use coarse grained molecular dynamics simulations to investigate diffusion properties of sheared lipid membranes with embedded transmembrane proteins. In membranes without proteins, we find normal in-plane diffusion of lipids in all flow…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
We propose a novel approach to detect the binding between proteins making use of the anomalous diffraction of natively present heavy elements inside the molecule 3D structure. In particular, we suggest considering sulfur atoms contained in…