Related papers: Simulating Mono-and Multi-Protein Phosphorylation …
It has been hypothesized that some form of "modular" structure in artificial neural networks should be useful for learning, compositionality, and generalization. However, defining and quantifying modularity remains an open problem. We cast…
Fluorescence microscopy reveals that the contents of many (membrane-free) nuclear "bodies" exchange rapidly with the soluble pool whilst the underlying structure persists; such observations await a satisfactory biophysical explanation. To…
A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…
A general method to obtain a representation of the structural landscape of nanoparticles in terms of a limited number of variables is proposed. The method is applied to a large dataset of parallel tempering molecular dynamics simulations of…
This paper presents a comprehensive analysis of simple models useful to analyze the growth of nanostructures obtained by cluster deposition. After detailing the potential interest of nanostructures, I extensively study the first stages of…
This paper introduces a new approach for simulating magnetic properties of nanocomposites comprising magnetic particles embedded in a non-magnetic matrix, taking into account the 3D structure of the system in which particles' positions…
Phosphorylation is a prototypical example of post-translational modifications (PTMs) that dynamically modulate protein func-tion, where dysregulation is often implicated in disease. NMR provides information on the exact location and time…
The activity of biological cells is primarily based on chemical reactions and typically modeled as a reaction-diffusion system. Cells are, however, highly crowded with macromolecules, including a variety of molecular machines such as…
Controlling the size distribution in the nucleation of copper particles is crucial for achieving nanocrystals with desired physical and chemical properties. However, their synthesis involves a complex system of solvents, ligands, and copper…
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
We apply a simulational proxy of the phi-value analysis and perform extensive mutagenesis experiments to identify the nucleating residues in the folding reactions of two small lattice Go polymers with different native geometries. These…
We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…
The physical and chemical properties of metal nanoparticles differ significantly from those of free metal atoms as well as from the properties of bulk metals, and therefore, they may be viewed as a transition regime between the two physical…
We describe a modification of the stochastic coupled cluster algorithm that allows the use of multiple reference determinants. By considering the secondary references as excitations of the primary reference and using them to change the…
In the cell, protein complexes form relying on specific interactions between their monomers. Excluded volume effects due to molecular crowding would lead to correlations between molecules even without specific interactions. What is the…
Computer simulation studies on the miscibility behavior and single chain properties in binary polymer blends are reviewed. We consider blends of various architectures in order to identify important architectural parameters on a coarse…
Background: If biology is modular then clusters, or communities, of proteins derived using only protein interaction network structure should define protein modules with similar biological roles. We investigate the link between biological…
Certain membrane proteins, peptides, nanoparticles and nanotubes have rigid structure and fixed shape. They are often viewed as spheres and cylinders with certain surface properties. Single Chain Mean Field theory is used to model the…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…