Related papers: Towards Experimental P-systems using multivesicula…
This paper studies the fusogenicity of cationic liposomes in relation to their surface distribution of cationic lipids and utilizes membrane phase separation to control this surface distribution. It is found that concentrating the cationic…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
Most biological molecules contain acido-basic groups that modulate their structure and interactions. A consequence is that pH gradients, local heterogeneities and dynamic variations are used by cells and organisms to drive or regulate…
Metamaterials made of periodic arrangements of electric permittivity and magnetic permeability and arrays of resonators can provide optic properties unexperienced in conventional materials, such as negative refractive index which can be…
We present LayerPCM, an extension of the polarizable-continuum model coupled to real-time time-dependent density-functional theory for an efficient and accurate description of the electrostatic interactions between molecules and…
Classical particle systems characterized by continuous size polydispersity, such as colloidal materials, are not straightforwardly described using statistical mechanics, since fundamental issues may arise from particle distinguishability.…
Porous structures are intricate solid materials with numerous small pores, extensively used in fields like medicine, chemical engineering, and aerospace. However, the design of such structures using computer-aided tools is a time-consuming…
Materials science inherently spans disciplines: experimentalists use advanced microscopy to uncover micro- and nanoscale structure, while theorists and computational scientists develop models that link processing, structure, and properties.…
We simulate a series of model polymer composites, composed of linear polymer strands and spherical, monodisperse filler particles (FP). These molecular dynamics simulations implement a coarse-grained, bead-spring force field and we vary…
Exploring and understanding the protein-folding problem has been a long-standing challenge in molecular biology. Here, using molecular dynamics simulation, we reveal how parallel distributed adjacent planar peptide groups of unfolded…
Formation and rupture of vesicles is a fundamental process underlying diverse phenomena in biology, materials science, and biomedical applications. Vesicles form when the area of a growing disk-like membrane exceeds a critical value at…
Computation biology helps to understand all processes in organisms from interaction of molecules to complex functions of whole organs. Therefore, there is a need for mathematical methods and models that deliver logical explanations in a…
We study numerically how multiple deformable capsules squeeze into a constriction. This situation is largely encountered in microfluidic chips designed to manipulate living cells, which are soft entities. We use fully three-dimensional…
We propose a very simple but realistic enough model which allows to include a large number of molecules in molecular dynamics MD simulations of these bilayers, but nevertheless taking into account molecular charge distributions, flexible…
In this paper we study a class of dynamical systems generated by iterations of multivariate permutation polynomial systems which lead to polynomial growth of the degrees of these iterations. Using these estimates and the same techniques…
Structure, function and dynamics of many biomolecular systems can be characterized by the energetic variational principle and the corresponding systems of partial differential equations (PDEs). This principle allows us to focus on the…
Lipid membranes form the barrier between the inside and outside of cells and many of their subcompartments. As such, they bind to a wide variety of nano- and micrometer sized objects and, in the presence of strong adhesive forces, strongly…
For natural frequency optimization of engineering structures, cellular composites have been shown to possess an edge over solid. However, existing multiscale design methods for cellular composites are either computationally exhaustive or…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…
We introduce a deterministic discrete-particle simulation approach, the Linearly-Transformed Particle-In-Cell (LTPIC) method, that employs linear deformations of the particles to reduce the noise traditionally associated with particle…