Related Research Articles
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion, the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials.
Dassault Systèmes Simulia Corp. is a computer-aided engineering (CAE) vendor. Formerly known as Abaqus Inc. and previously Hibbitt, Karlsson & Sorensen, Inc., (HKS), the company was founded in 1978 by David Hibbitt, Bengt Karlsson and Paul Sorensen, and has its headquarters in Providence, Rhode Island.
BIOVIA is a software company headquartered in the United States, with representation in Europe and Asia. It provides software for chemical, materials and bioscience research for the pharmaceutical, biotechnology, consumer packaged goods, aerospace, energy and chemical industries.
The William O. Baker Award for Initiatives in Research, previously the NAS Award for Initiatives in Research, is awarded annually by the National Academy of Sciences "to recognize innovative young scientists and to encourage research likely to lead toward new capabilities for human benefit. The award is to be given to a citizen of the United States, preferably no older than 35 years of age. The field of presentation rotates among the physical sciences, engineering, and mathematics."
This is a list of computer programs that are predominantly used for molecular mechanics calculations.
Chemical Computing Group is a software company specializing in research software for computational chemistry, bioinformatics, cheminformatics, docking, pharmacophore searching and molecular simulation. The company's main customer base consists of pharmaceutical and biotechnology companies, as well as academic research groups. It is a private company that was founded in 1994; it is based in Montreal, Quebec, Canada. Its main product, Molecular Operating Environment (MOE), is written in a self-contained programming system, the Scientific Vector Language (SVL).
The following outline is provided as an overview of and topical guide to nanotechnology:
Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo.
Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It provides a graphical environment for the common programs of quantum and classical molecular modelling ORCA, NWChem, Firefly, CP2K and MDynaMix . The molecular mechanics calculations cover model building, energy optimizations and molecular dynamics. Firefly covers a wide range of quantum chemistry methods. Ascalaph Designer is free and open-source software, released under the GNU General Public License, version 2 (GPLv2).
Molecular models of DNA structures are representations of the molecular geometry and topology of deoxyribonucleic acid (DNA) molecules using one of several means, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. These representations include closely packed spheres made of plastic, metal wires for skeletal models, graphic computations and animations by computers, artistic rendering. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Ninithi is free and open source modelling software that can be used to visualize and analyze carbon materials used in nanotechnology. Users of ninithi can visualize the 3D molecular geometries of graphene/nano-ribbons, carbon nanotubes and fullerenes. Ninithi also provides features to simulate the electronic band structures of graphene and carbon nanotubes. The software was developed by Lanka Software Foundation, in Sri Lanka and released in 2010 under the GPL licence. Ninithi is written in the Java programming language and available for both Microsoft Windows and Linux platforms.
Discovery Studio is a suite of software for simulating small molecule and macromolecule systems. It is developed and distributed by Dassault Systemes BIOVIA.
Scigress, stylized SCiGRESS, is a software suite for molecular modelling, computational chemistry, drug design, and materials science, a successor to Computer Aided Chemistry (CAChe) software.
Massively Parallel Monte Carlo (MPMC) is a Monte Carlo method package primarily designed to simulate liquids, molecular interfaces, and functionalized nanoscale materials. It was developed originally by Jon Belof and is now maintained by a group of researchers in the Department of Chemistry and SMMARTT Materials Research Center at the University of South Florida. MPMC has been applied to the scientific research challenges of nanomaterials for clean energy, carbon sequestration, and molecular detection. Developed to run efficiently on the most powerful supercomputing platforms, MPMC can scale to extremely large numbers of CPUs or GPUs. Since 2012, MPMC has been released as an open-source software project under the GNU General Public License (GPL) version 3, and the repository is hosted on GitHub.
SAMSON is a computer software platform for molecular design being developed by OneAngstrom and previously by the NANO-D group at the French Institute for Research in Computer Science and Automation (INRIA).
Molecular Operating Environment is a drug discovery software platform that integrates visualization, modeling and simulations, as well as methodology development, in one package. MOE scientific applications are used by biologists, medicinal chemists and computational chemists in pharmaceutical, biotechnology and academic research. MOE runs on Windows, Linux, Unix, and macOS. Main application areas in MOE include structure-based design, fragment-based design, pharmacophore discovery, medicinal chemistry applications, biologics applications, protein and antibody modeling, molecular modeling and simulations, cheminformatics & QSAR. The Scientific Vector Language (SVL) is the built-in command, scripting and application development language of MOE.
MBN Explorer is a software package for molecular dynamics simulations, structure optimization and kinetic Monte Carlo simulations. It is designed for multiscale computational analysis of structure and dynamics of atomic clusters and nanoparticles, biomolecules and nanosystems, nanostructured materials, different states of matter and various interfaces. The software has been developed by MBN Research Center.
Computational materials science and engineering uses modeling, simulation, theory, and informatics to understand materials. The main goals include discovering new materials, determining material behavior and mechanisms, explaining experiments, and exploring materials theories. It is analogous to computational chemistry and computational biology as an increasingly important subfield of materials science.
In the context of chemistry and molecular modelling, the Interface force field (IFF) is a force field for classical molecular simulations of atoms, molecules, and assemblies up to the large nanometer scale, covering compounds from across the periodic table. It employs a consistent classical Hamiltonian energy function for metals, oxides, and organic compounds, linking biomolecular and materials simulation platforms into a single platform. The reliability is often higher than that of density functional theory calculations at more than a million times lower computational cost. IFF includes a physical-chemical interpretation for all parameters as well as a surface model database that covers different cleavage planes and surface chemistry of included compounds. The Interface Force Field is compatible with force fields for the simulation of primarily organic compounds and can be used with common molecular dynamics and Monte Carlo codes. Structures and energies of included chemical elements and compounds are rigorously validated and property predictions are up to a factor of 100 more accurate relative to earlier models.
References
- ↑ "Materials Studio References". DS BIOVIA. Dassault Systèmes BIOVIA. Retrieved 24 January 2017.
- ↑ "Materials Studio - Updates". DS BIOVIA. Dassault Systèmes BIOVIA. Archived from the original on 2 February 2017. Retrieved 24 January 2017.
- ↑ BIOVIA Materials Studio overview, BIOVIA website
- ↑ "NDSU CHPC/Software/MS Home Page". Archived from the original on 27 September 2007.
- ↑ DMol3