This document is the deliverable 1.3 of French ANR CALAMAR. It presents a study of different formalisms used for modelling and analyzing large molecular regulation networks, their formal links, in terms of mutual encodings and of abstractions, and the corresponding levels of detail captured. Key-words: regulation networks, expressivity, abstraction, formalisms, modelling ANR CALAMAR ANR-08-SYSC...

This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types ...

Polymers are unique among engineering materials since they are the only common technological material in which the amorphous state can be the minimum energy state. This is a consequence of topology. Molecular topology is a description of molecules which includes their stereo-chemical arrangement, branching, formation of helices and network/looping/entanglement characteristics. Consider two chai...

Single-cell RNA sequencing (scRNA-Seq) is a revolutionary technology, which allows studying fundamental biological questions that were previously out of reach [1, 2]. It allows, for the first time, to reveal a cell’s identity and characterize its molecular circuitry in an unbiased, data-driven way. The product of a scRNA-Seq experiment is a data matrix X where entry Xng approximates the number ...

We measure electron tunneling in single-molecule transistors made from C140, a molecule with a mass-spring-mass geometry chosen as a model system to study electron-vibration coupling. We observe vibration-assisted tunneling at an energy corresponding to the stretching mode of C140. Molecular modeling provides explanations for why this mode couples more strongly to electron tunneling than the ot...

We demonstrate an automatic method of force field development for molecular simulations. Parameter tuning is taken as an optimization problem in many dimensions. The parameters are automatically adapted to reproduce known experimental data such as the density and the heat of vaporization. Our method is more systematic than guessing parameters and, at the same time saves human labour in paramete...

2014 A few lines have been observed in the far ultraviolet emission spectrum of molecular hydrogen and deuterium. They are assigned to transitions from levels of the 3p03C0D 103A0 ustate, lying above the dissociation limit into H(ls) + H(n = 2), near 84.5 nm, and, for some of them, above the first ionization limit near 80.4 nm, the lower state being X 103A3g+ (v" = 1). This is in fair agreement...

Modeling of molecular interactions is increasingly used in life science research and biotechnology development. Examples are computer aided drug design, prediction of protein interactions with other molecules, and simulation of networks of biomolecules in a particular process in human body. This article reviews recent progress in the related fields and provides a brief overview on the methods u...

Hesperidin is a flavonone glycoside found in sweet orange and is effectively used in treatment for pain and disease. Although it plays a big role in the pharmaceutical area, hesperidin has a poor water soluble property. β-cyclodextrin (β-CD), a macrocyclic host with hydrophobic cavity and hydrophilic outer surface is a common pharmaceutical application to enhance the solubility, stability, safe...