Related papers: Simulated single molecule microscopy with SMeagol
Synthetic biology brings together concepts and techniques from engineering and biology. In this field, computer-aided design (CAD) is necessary in order to bridge the gap between computational modeling and biological data. An application…
Simulated annealing (SA) was inspired from annealing in metallurgy, a technique involving heating and controlled cooling of a material to increase the size of its crystals and reduce their defects, both are attributes of the material that…
In our previous work, we demonstrated that it is feasible to perform analysis on mutation signature data without the need for downloads or installations and analyze individual patient data at scale without compromising privacy. Building on…
Continuum robots are advancing bronchoscopy procedures by accessing complex lung airways and enabling targeted interventions. However, their development is limited by the lack of realistic training and test environments: Real data is…
Spectroscopy is the most important method for probing the structure of molecules. However, predicting molecular spectra on classical computers is computationally expensive, with the most accurate methods having a cost that grows…
In almost 30 years of PEM fuel cell modeling, countless numerical models have been developed in science and industrial applications, almost none of which have been fully disclosed to the public. There is a large need for standardization and…
We introduce NebulOS, a Big Data platform that allows a cluster of Linux machines to be treated as a single computer. With NebulOS, the process of writing a massively parallel program for a datacenter is no more complicated than writing a…
We present basic informations about package SPHOTOM for an automatic multicolour photometry. This package is in development for a creation of photometric pipe-line, which we plan to use in near future with our new instruments. It could…
Realistic simulations of detailed, biophysics-based, multi-scale models require very high resolution and, thus, large-scale compute facilities. Existing simulation environments, especially for biomedical applications, are designed to allow…
Light-ion microbeams provide a unique opportunity to irradiate biological samples at the cellular level and to investigate radiobiological effects at low doses of high LET ionising radiation. Since 1998 a single-ion irradiation facility has…
Single-cell technologies have revolutionized biomedical research by enabling scalable measurement of the genome, transcriptome, and proteome of multiple systems at single-cell resolution. Now widely applied to cancer models, these assays…
We present MRSeqStudio, a new all-in-one web-based tool for MRI sequence development and simulation, with the physics-based simulator KomaMRI running at the back-end and our own sequence designer at the front-end. It combines accessibility,…
We introduce a Markov Chain Monte Carlo simulation and data analysis package for the cosmological computation package Cmbeasy. We have taken special care in implementing an adaptive step algorithm for the Markov Chain Monte Carlo in order…
We compare the ability of a simulated annealing program and an evolutionary algorithm to find molecules with large molecular average hyperpolarizabilities. This property is an important component of nonlinear optical materials. Both…
Simulations of scanning tunneling microscopy measurements for molecules on surfaces are traditionally based on a perturbative approach, most typically employing the Tersoff-Hamann method. This assumes that the STM tip is far from the sample…
Single cell analysis of skeletal muscle (SM) tissue is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images…
Heterogeneous multiscale methods (HMM) combine molecular accuracy of particle-based simulations with the computational efficiency of continuum descriptions to model flow in soft matter liquids. In these schemes, molecular simulations…
For the self-consistent description of various plasma sources operated in the low-pressure (nonlocal, kinetic) regime, the Particle-In-Cell simulation approach, combined with the Monte Carlo treatment of collision processes (PIC/MCC), has…
This paper presents the simulation of the GLAST high energy gamma-ray telescope. The simulation package, written in C++, is based on the Geant4 toolkit, and it is integrated into a general framework used to process events. A detailed…
In our current era, numerical simulations have become indispensable theoretical and experimental tools for use in daily research activities, particularly in the materials science fields. However, the installation processes for such…