相关论文: Molecular multiresolution surfaces
We introduce a novel concept, the minimal molecular surface (MMS), as a new paradigm for the theoretical modeling of biomolecule-solvent interfaces. When a less polar macromolecule is immersed in a polar environment, the surface free energy…
A multi-scale framework was recently proposed for more realistic molecular dynamics simulations in continuum solvent models by coupling a molecular mechanics treatment of solute with a fluid mechanics treatment of solvent, where we…
In the calculation of thermodynamic properties and three dimensional structures of macromolecules, such as proteins, it is important to have a good algorithm for computing solvent accessible surface area of macromolecules. Here we propose a…
We derive the equations that describe adsorption of diffusing particles onto a surface followed by additional surface kinetic steps before being transported across the interface. Multistage surface kinetics occurs during membrane protein…
Since its foundations, more than one hundred years ago, the field of structural biology has strived to understand and analyze the properties of molecules and their interactions by studying the structure that they take in 3D space. However,…
Spherical multi-layered structures are prevalent in numerous biological systems and engineered applications, including tumor spheroids, layered tissues, and multi-shell nanoparticles for targeted drug delivery. Despite their widespread…
Spectral imaging is a fundamental diagnostic technique with widespread application. Conventional spectral imaging approaches have intrinsic limitations on spatial and spectral resolutions due to the physical components they rely on. To…
Recently, we introduced Relative Resolution as a hybrid formalism for fluid mixtures [1]. The essence of this approach is that it switches molecular resolution in terms or relative separation: While nearest neighbors are characterized by a…
Computational multiscale modeling encompasses a wide range of end-products and a great number of technological applications. This paper provides an overview of the computational multiscale modeling approach based on the utilization of MBN…
This article examines recent research in molecular communications from a telecommunications system design perspective. In particular, it focuses on channel models and state-of-the-art physical layer techniques. The goal is to provide a…
Optical multiplexing is a key technique that enhances the capacity of optical systems by independently modulating various optical parameters to carry distinct information. Among these parameters, wavelength, polarization, and angle are the…
Deep learning is changing many areas in molecular physics, and it has shown great potential to deliver new solutions to challenging molecular modeling problems. Along with this trend arises the increasing demand of expressive and versatile…
For the study of complex synthetic and biological molecular systems by computer simulations one is still restricted to simple model systems or to by far too small time scales. To overcome this problem multiscale techniques are being…
Molecular docking is an essential tool for drug design. It helps the scientist to rapidly know if two molecules, respectively called ligand and receptor, can be combined together to obtain a stable complex. We propose a new multi-objective…
The identification of the interfacial molecules in fluid-fluid equilibrium is a long-standing problem in the area of simulation. We here propose a new point of view, making use of concepts taken from the field of computational geometry,…
Combined-resolution simulations are an effective way to study molecular properties across a range of length- and time-scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size…
We consider radially symmetric capillary surfaces that are described by bounded generating curves. We use the arc-length representation of the differential equations for these surfaces to allow for vertical points and inflection points…
In this paper the full and exhaustive algorithm of formation of a smooth molecular Solvent Excluded Surface- SES, and also Solvent Accessible Surface- SAS is presented. These surfaces are a boundary between molecule and solvent. The basis…
Developable surfaces are commonly observed in various applications such as architecture, product design, manufacturing, mechanical materials, and data physicalization as well as in the development of tangible interaction and deformable…
Morphological change of bilayer membrane in vivo is not a spontaneous procedure but modulated by various types of proteins in general. Most of these modulations are associated with the localization of related proteins in the crowded lipid…