10,908 research outputs found
Instant visualization of secondary structures of molecular models
Molecular Dynamics simulations are of key importance in the drug design field. Among all possible representations commonly used to inspect these simulations, Ribbons has the advantage of giving the expert a good overview of the conformation of the molecule. Although several techniques have been previously proposed to render ribbons, all of them have limitations in terms of space or calculation time, making them not suitable for real-time interaction with simulation software. In this paper we present a novel adaptive method that generates ribbons in real-time, taking advantage of the tessellation shader. The result is a fast method that requires no precomputation,
and that generates high quality shapes and shading.This work has been supported by the projects TIN2013-47137-C2-1-P and TIN2014-52211-C2-1-R of the Spanish
Ministerio de Economía y Competitividad, and the project 2014-SGR 146 from the Catalan Government.Postprint (author's final draft
Physics-based visual characterization of molecular interaction forces
Molecular simulations are used in many areas of biotechnology, such as drug design and enzyme engineering. Despite the development of automatic computational protocols, analysis of molecular interactions is still a major aspect where human comprehension and intuition are key to accelerate, analyze, and propose modifications to the molecule of interest. Most visualization algorithms help the users by providing an accurate depiction of the spatial arrangement: the atoms involved in inter-molecular contacts. There are few tools that provide visual information on the forces governing molecular docking. However, these tools, commonly restricted to close interaction between atoms, do not consider whole simulation paths, long-range distances and, importantly, do not provide visual cues for a quick and intuitive comprehension of the energy functions (modeling intermolecular interactions) involved. In this paper, we propose visualizations designed to enable the characterization of interaction forces by taking into account several relevant variables such as molecule-ligand distance and the energy function, which is essential to understand binding affinities. We put emphasis on mapping molecular docking paths obtained from Molecular Dynamics or Monte Carlo simulations, and provide time-dependent visualizations for different energy components and particle resolutions: atoms, groups or residues. The presented visualizations have the potential to support domain experts in a more efficient drug or enzyme design process.Peer ReviewedPostprint (author's final draft
The Geant4-DNA project
The Geant4-DNA project proposes to develop an open-source simulation software
based and fully included in the general-purpose Geant4 Monte Carlo simulation
toolkit. The main objective of this software is to simulate biological damages
induced by ionising radiation at the cellular and sub-cellular scale. This
project was originally initiated by the European Space Agency for the
prediction of deleterious effects of radiation that may affect astronauts
during future long duration space exploration missions. In this paper, the
Geant4-DNA collaboration presents an overview of the whole ongoing project,
including its most recent developments already available in the last Geant4
public release (9.3 BETA), as well as an illustration example simulating the
direct irradiation of a chromatin fibre. Expected extensions involving several
research domains, such as particle physics, chemistry and cellular and
molecular biology, within a fully interdiciplinary activity of the Geant4
collaboration are also discussed.Comment: presented by S. Incerti at the ASIA SIMULATION CONFERENCE 2009,
October 7-9, 2009, Ritsumeikan University, Shiga, Japa
Simultaneous Coherent Structure Coloring facilitates interpretable clustering of scientific data by amplifying dissimilarity
The clustering of data into physically meaningful subsets often requires
assumptions regarding the number, size, or shape of the subgroups. Here, we
present a new method, simultaneous coherent structure coloring (sCSC), which
accomplishes the task of unsupervised clustering without a priori guidance
regarding the underlying structure of the data. sCSC performs a sequence of
binary splittings on the dataset such that the most dissimilar data points are
required to be in separate clusters. To achieve this, we obtain a set of
orthogonal coordinates along which dissimilarity in the dataset is maximized
from a generalized eigenvalue problem based on the pairwise dissimilarity
between the data points to be clustered. This sequence of bifurcations produces
a binary tree representation of the system, from which the number of clusters
in the data and their interrelationships naturally emerge. To illustrate the
effectiveness of the method in the absence of a priori assumptions, we apply it
to three exemplary problems in fluid dynamics. Then, we illustrate its capacity
for interpretability using a high-dimensional protein folding simulation
dataset. While we restrict our examples to dynamical physical systems in this
work, we anticipate straightforward translation to other fields where existing
analysis tools require ad hoc assumptions on the data structure, lack the
interpretability of the present method, or in which the underlying processes
are less accessible, such as genomics and neuroscience
Structures in stratified plane mixing layers and the effects of cross-shear
A two-dimensional temporal mixing layer is generated in a stratified tilting tank similar to that used by Thorpe (1968). Extensive flow dynamics visualization is carried out using, for the top and bottom layers, fluids of different densities but of the same index of refraction. The two-dimensional density field is measured with the laser-induced fluorescence technique (LIF). The study examines further the classical problem of the two-dimensional mixing layer and explores the effects of cross-shear on a nominally two-dimensional mixing layer, a situation widespread in complex industrial and natural flows. Cross-shear is another component of shear, in plane with but perpendicular to the main shear of the base flow, generated by tilting the tank around a second axis
Dynamic Influence Networks for Rule-based Models
We introduce the Dynamic Influence Network (DIN), a novel visual analytics
technique for representing and analyzing rule-based models of protein-protein
interaction networks. Rule-based modeling has proved instrumental in developing
biological models that are concise, comprehensible, easily extensible, and that
mitigate the combinatorial complexity of multi-state and multi-component
biological molecules. Our technique visualizes the dynamics of these rules as
they evolve over time. Using the data produced by KaSim, an open source
stochastic simulator of rule-based models written in the Kappa language, DINs
provide a node-link diagram that represents the influence that each rule has on
the other rules. That is, rather than representing individual biological
components or types, we instead represent the rules about them (as nodes) and
the current influence of these rules (as links). Using our interactive DIN-Viz
software tool, researchers are able to query this dynamic network to find
meaningful patterns about biological processes, and to identify salient aspects
of complex rule-based models. To evaluate the effectiveness of our approach, we
investigate a simulation of a circadian clock model that illustrates the
oscillatory behavior of the KaiC protein phosphorylation cycle.Comment: Accepted to TVCG, in pres
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Digitizing mass spectrometry data to explore the chemical diversity and distribution of marine cyanobacteria and algae.
Natural product screening programs have uncovered molecules from diverse natural sources with various biological activities and unique structures. However, much is yet underexplored and additional information is hidden in these exceptional collections. We applied untargeted mass spectrometry approaches to capture the chemical space and dispersal patterns of metabolites from an in-house library of marine cyanobacterial and algal collections. Remarkably, 86% of the metabolomics signals detected were not found in other available datasets of similar nature, supporting the hypothesis that marine cyanobacteria and algae possess distinctive metabolomes. The data were plotted onto a world map representing eight major sampling sites, and revealed potential geographic locations with high chemical diversity. We demonstrate the use of these inventories as a tool to explore the diversity and distribution of natural products. Finally, we utilized this tool to guide the isolation of a new cyclic lipopeptide, yuvalamide A, from a marine cyanobacterium
Interface-controlled creep in metallic glass composites
In this work we present molecular dynamics simulations on the creep behavior
of metallic glass composites. Surprisingly, all composites
exhibit much higher creep rates than the homogeneous glass. The glass-crystal
interface can be viewed as a weak interphase, where the activation barrier of
shear transformation zones is lower than in the surrounding glass. We observe
that the creep behavior of the composites does not only depend on the interface
area but also on the orientation of the interface with respect to the loading
axis. We propose an explanation in terms of different mean Schmid factors of
the interfaces, with the amorphous interface regions acting as preferential
slip sites.Comment: 11 pages, 13 figure
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