• CP2K

  • Referenced in 8 articles [sw15391]
  • that can perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological ... waves approaches GPW and GAPW. Supported theory levels include DFTB, LDA, GGA, MP2, RPA, semi ... simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy...
  • Rallpacks

  • Referenced in 6 articles [sw18102]
  • point where there are several general-purpose simulators to choose from. These cater to various ... neuronal models, which range from the molecular level to descriptions of entire sensory modalities ... addition, there are numerous custom-designed simulations, adaptations of electrical circuit simulators, and other specific...
  • OpenAtom

  • Referenced in 2 articles [sw22267]
  • portable parallel application for molecular dynamics simulations at the quantum level. It is written using...
  • PORGY

  • Referenced in 14 articles [sw06923]
  • molecular networks, adhoc communication networks or interaction nets. The ability to act on the simulation ... graph rewriting systems into a high-level visual programming environment...
  • DFTBaby

  • Referenced in 1 article [sw20326]
  • running non-adiabatic molecular dynamics simulations at the level of charge-consistent tight-binding ... These quantities are fed into a molecular dynamics code, which integrates Newton’s equations...
  • ZIFA

  • Referenced in 13 articles [sw32141]
  • states through molecular characterization of gene expression on the single cell level. Dimensionality reduction ... show that it improves modeling accuracy on simulated and biological data sets...
  • Kwant

  • Referenced in 8 articles [sw19547]
  • even those entirely written in the low level FORTRAN and C/C++ languages. Tight-binding models ... used to simulate metals, graphene, topological insulators, quantum Hall effect, superconductivity, spintronics, molecular electronics...
  • OpenQEMIST

  • Referenced in 1 article [sw33444]
  • designed to enable the accurate calculation of molecular properties by leveraging advanced problem decomposition ... techniques implemented in QEMIST enables massively parallel simulations by breaking down a computational chemistry task ... achieve a higher level of accuracy for large-scale, practical molecular simulations...
  • MapSplice

  • Referenced in 6 articles [sw31868]
  • TopHat and SpliceMap on a set of simulated RNA-seq data. Experimental studies also support ... global level as well as the differences between molecular subtypes of breast cancer. These combined...
  • Ribosome Builder

  • Referenced in 1 article [sw10930]
  • Ribosome Builder: a software project to simulate the ribosome. The Ribosome Builder is a software ... allows the user to assemble the multiple molecular components within a 3D space ... level of detail. The program employs a simplified molecular dynamics forcefield that can simulate...
  • someMTP

  • Referenced in 5 articles [sw11118]
  • hypotheses, which are tested at the uncorrected level q until a suitable number ... under arbitrary dependence. It is shown in simulation that we compare particularly well when ... conclude with an application to identification of molecular signatures of intracranial ependymoma. The methods...
  • PuReMD

  • Referenced in 3 articles [sw18042]
  • community code, PuReMD, for reactive molecular dynamics simulations using the ReaxFF force field. PuReMD ... simulating diverse systems ranging from biomembranes to explosives (RDX) at atomistic level of detail...
  • BioJADE

  • Referenced in 1 article [sw20853]
  • BioJADE: A Design and Simulation Tool for Synthetic Biological Systems. The next generations of both ... that control be exerted at the molecular level. Creating, characterizing and controlling synthetic biological systems ... synthesizing systems, but also designing and simulating them. The BioJADE project provides a comprehensive, extensible...
  • YASARA

  • Referenced in 2 articles [sw27635]
  • workstations. YASARA is a molecular-graphics, -modeling and -simulation program for Windows, Linux, MacOS ... input devices, YASARA creates a new level of interaction with the ’artificial reality’, that allows...
  • ExaBayes

  • Referenced in 2 articles [sw23048]
  • allows biologists to collect the entirety of molecular evidence for reconstructing evolutionary trees. We introduce ... whole-genome level using the SuperMUC supercomputer and simulated data...
  • StochPy

  • Referenced in 7 articles [sw27252]
  • from the novice users and offers low-level programming access to the experienced user. Here ... tool for stochastic simulation in cell biology. It provides various stochastic simulation algorithms, SBML support ... statistical functions and plotting facilities for stochastic simulations. We illustrate the functionality of StochPy with ... comprehensive software package for stochastic simulation of the molecular control networks of living cells...
  • Simbio

  • Referenced in 2 articles [sw09096]
  • simBio is a simulator for biological systems such as cardiac cells, epithelial cells, and pancreatic ... biology, extensive research results regarding molecular and cellular level functions have been accumulated...
  • MesoBioNano

  • Referenced in 1 article [sw18198]
  • universal program for multiscale computer simulations of complex molecular structure and dynamics. We present ... package allows to model molecular systems of varied level of complexity. In particular, MBN Explorer...
  • VirtualLeaf

  • Referenced in 4 articles [sw28766]
  • mechanics. The multilevel regulatory mechanisms complicate classic molecular genetics or functional genomics approaches to biological ... relation between genes and traits at the level of the whole plant or organ. Instead ... regulation networks”) required for setting up a simulation and present those to the user...
  • nMoldyn

  • Referenced in 2 articles [sw07359]
  • neutron scattering oriented analysis of molecular dynamics simulations We present a new implementation ... decomposition of neutron scattering intensities from Molecular Dynamics trajectories (Comp. Phys. Commun ... possible by the use of a high-level language, Python, and of modern object-oriented ... powerful feature that allows to relate simulation results to theoretical studies. © 2003 Wiley Periodicals...