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Computational chemistry is a branch of chemistry that uses computer simulations 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. The importance of this subject stems from the fact that, with the exception of some relatively recent findings related to the hydrogen molecular ion, achieving an accurate quantum mechanical depiction of chemical systems analytically, or in a closed form, is not feasible. The complexity inherent in the many-body problem exacerbates the challenge of providing detailed descriptions of quantum mechanical systems. While computational results normally complement information obtained by chemical experiments, it can occasionally predict unobserved chemical phenomena.
In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. It does not assume or postulate any natural laws, but explains the macroscopic behavior of nature from the behavior of such ensembles.
Density-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density. DFT is among the most popular and versatile methods available in condensed-matter physics, computational physics, and computational chemistry.
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit, or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons.
PLATO is a suite of programs for electronic structure calculations. It receives its name from the choice of basis set used to expand the electronic wavefunctions.
The Vienna Ab initio Simulation Package, better known as VASP, is a package written primarily in Fortran for performing ab initio quantum mechanical calculations using either Vanderbilt pseudopotentials, or the projector augmented wave method, and a plane wave basis set. The basic methodology is density functional theory (DFT), but the code also allows use of post-DFT corrections such as hybrid functionals mixing DFT and Hartree–Fock exchange, many-body perturbation theory and dynamical electronic correlations within the random phase approximation (RPA) and MP2.
Koopmans' theorem states that in closed-shell Hartree–Fock theory (HF), the first ionization energy of a molecular system is equal to the negative of the orbital energy of the highest occupied molecular orbital (HOMO). This theorem is named after Tjalling Koopmans, who published this result in 1934.
In the context of chemistry, molecular physics and physical chemistry and molecular modelling, a force field is a computational model that is used to describe the forces between atoms within molecules or between molecules as well as in crystals. Force fields are a variety of interatomic potentials. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of the atomistic level. Force fields are usually used in molecular dynamics or Monte Carlo simulations. The parameters for a chosen energy function may be derived from classical laboratory experiment data, calculations in quantum mechanics, or both. Force fields utilize the same concept as force fields in classical physics, with the main difference that the force field parameters in chemistry describe the energy landscape on the atomistic level. From a force field, the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates.
Spartan is a molecular modelling and computational chemistry application from Wavefunction. It contains code for molecular mechanics, semi-empirical methods, ab initio models, density functional models, post-Hartree–Fock models, and thermochemical recipes including G3(MP2) and T1. Quantum chemistry calculations in Spartan are powered by Q-Chem.
Car–Parrinello molecular dynamics or CPMD refers to either a method used in molecular dynamics or the computational chemistry software package used to implement this method.
CP2K is a freely available (GPL) quantum chemistry and solid state physics program package, written in Fortran 2008, to perform atomistic simulations of solid state, liquid, molecular, periodic, material, crystal, and biological systems. It provides a general framework for different methods: density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW) via LDA, GGA, MP2, or RPA levels of theory, classical pair and many-body potentials, semi-empirical and tight-binding Hamiltonians, as well as Quantum Mechanics/Molecular Mechanics (QM/MM) hybrid schemes relying on the Gaussian Expansion of the Electrostatic Potential (GEEP). The Gaussian and Augmented Plane Waves method (GAPW) as an extension of the GPW method allows for all-electron calculations. CP2K can do simulations of molecular dynamics, metadynamics, Monte Carlo, Ehrenfest dynamics, vibrational analysis, core level spectroscopy, energy minimization, and transition state optimization using NEB or dimer method.
David Matthew Ceperley is a theoretical physicist in the physics department at the University of Illinois Urbana-Champaign or UIUC. He is a world expert in the area of Quantum Monte Carlo computations, a method of calculation that is generally recognised to provide accurate quantitative results for many-body problems described by quantum mechanics.
Yambo is a computer software package for studying many-body theory aspects of solids and molecule systems. It calculates the excited state properties of physical systems from first principles, e.g., from quantum mechanics law without the use of empirical data. It is an open-source software released under the GNU General Public License (GPL). However the main development repository is private and only a subset of the features available in the private repository are cloned into the public repository and thus distributed.
MADNESS is a high-level software environment for the solution of integral and differential equations in many dimensions using adaptive and fast harmonic analysis methods with guaranteed precision based on multiresolution analysis and separated representations .
In biophysics and related fields, reduced dimension forms (RDFs) are unique on-off mechanisms for random walks that generate two-state trajectories (see Fig. 1 for an example of a RDF and Fig. 2 for an example of a two-state trajectory). It has been shown that RDFs solve two-state trajectories, since only one RDF can be constructed from the data, where this property does not hold for on-off kinetic schemes, where many kinetic schemes can be constructed from a particular two-state trajectory (even from an ideal on-off trajectory). Two-state time trajectories are very common in measurements in chemistry, physics, and the biophysics of individual molecules (e.g. measurements of protein dynamics and DNA and RNA dynamics, activity of ion channels, enzyme activity, quantum dots ), thus making RDFs an important tool in the analysis of data in these fields.
Michele Parrinello is an Italian physicist particularly known for his work in molecular dynamics. Parrinello and Roberto Car were awarded the Dirac Medal of the International Centre for Theoretical Physics (ICTP) and the Sidney Fernbach Award in 2009 for their continuing development of the Car–Parrinello method, first proposed in their seminal 1985 paper, "Unified Approach for Molecular Dynamics and Density-Functional Theory". They have continued to receive awards for this breakthrough, most recently the Dreyfus Prize in the Chemical Sciences and the 2020 Benjamin Franklin Medal in Chemistry.
BigDFT is a free software package for physicists and chemists, distributed under the GNU General Public License, whose main program allows the total energy, charge density, and electronic structure of systems made of electrons and nuclei to be calculated within density functional theory (DFT), using pseudopotentials, and a wavelet basis.
Interatomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space. Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties. Examples of quantitative properties and qualitative phenomena that are explored with interatomic potentials include lattice parameters, surface energies, interfacial energies, adsorption, cohesion, thermal expansion, and elastic and plastic material behavior, as well as chemical reactions.
Mixed quantum-classical (MQC) dynamics is a class of computational theoretical chemistry methods tailored to simulate non-adiabatic (NA) processes in molecular and supramolecular chemistry. Such methods are characterized by:
- Propagation of nuclear dynamics through classical trajectories;
- Propagation of the electrons through quantum methods;
- A feedback algorithm between the electronic and nuclear subsystems to recover nonadiabatic information.
Noa Marom is an Israeli materials scientist and computational physicist at Carnegie Mellon University. She was awarded the International Union of Pure and Applied Physics Young Scientist Prize.
References
- ↑ "Physics - Neepa T. Maitra". physics.aps.org. Retrieved 2024-01-12.
- ↑ "Prof. Neepa Maitra – Maitra Group" . Retrieved 2024-01-12.
- ↑ "Physics - Neepa T. Maitra". physics.aps.org. Retrieved 2019-03-04.
- ↑ "Alumni". www-heller.harvard.edu. Retrieved 2019-03-04.
- ↑ "Physics Faculty and Staff Directory". Rutgers SAS-Newark. Retrieved 2024-03-20.
- 1 2 3 "Projects – Maitra Group" . Retrieved 2024-03-20.
- ↑ "CECAM - Triggering out-of-equilibrium dynamics in molecular systemsTriggering out-of-equilibrium dynamics in molecular systems". www.cecam.org. Retrieved 2024-03-20.
- ↑ "Invited speakers - PNGF8 Aug 7-11 2023". www.oru.se. Retrieved 2024-03-20.
- ↑ "NSF Award Search: Award#0547913 - CAREER: Time-Dependent Density Functional Theory for Atoms, Molecules, and Quantum Dots". www.nsf.gov. Retrieved 2019-03-04.
- ↑ "NSF Award Search: Award # 2154829 - Molecules in Classical and Quantized Fields: Developing Time-dependent Density Functional and Exact Factorization Methods for Electrons, Ions, and Photons". www.nsf.gov. Retrieved 2024-01-12.
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