Leslie Victor Woodcock (born 20 May 1945, Batley) [1] is Emeritus Professor of Chemical Thermodynamics at the University of Manchester. He has also held appointments at the University of Cambridge, the University of Amsterdam, and the University of Bradford. He has worked with simulations for the U.S. Air Force. [2] [3]
Woodcock received his Ph.D. in London in 1970. [4] His work in the field of molecular dynamics includes one of the first simulations of ionic liquids [5] and development of the WAC model of liquid silica. [6] [7]
Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields. The method is applied mostly in chemical physics, materials science, and biophysics.
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia.
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.
In biology and other experimental sciences, an in silico experiment is one performed on computer or via computer simulation. The phrase is pseudo-Latin for 'in silicon', referring to silicon in computer chips. It was coined in 1987 as an allusion to the Latin phrases in vivo, in vitro, and in situ, which are commonly used in biology. The latter phrases refer, respectively, to experiments done in living organisms, outside living organisms, and where they are found in nature.
Stuart Alan Rice is an American theoretical chemist and physical chemist. He is well known as a theoretical chemist who also does experimental research, having spent much of his career working in multiple areas of physical chemistry. He is currently the Frank P. Hixon Distinguished Service Professor Emeritus at the University of Chicago. During his tenure at the University of Chicago, Rice has trained more than 100 Ph.D. students and postdoctoral researchers. He received the National Medal of Science in 1999.
In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both. Force fields are interatomic potentials and utilize the same concept as force fields in classical physics, with the difference that the force field parameters in chemistry describe the energy landscape, from which the acting forces on every particle are derived as a gradient of the potential energy with respect to the particle coordinates.
In computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
Dissipative particle dynamics (DPD) is an off-lattice mesoscopic simulation technique which involves a set of particles moving in continuous space and discrete time. Particles represent whole molecules or fluid regions, rather than single atoms, and atomistic details are not considered relevant to the processes addressed. The particles' internal degrees of freedom are integrated out and replaced by simplified pairwise dissipative and random forces, so as to conserve momentum locally and ensure correct hydrodynamic behaviour. The main advantage of this method is that it gives access to longer time and length scales than are possible using conventional MD simulations. Simulations of polymeric fluids in volumes up to 100 nm in linear dimension for tens of microseconds are now common.
Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations.
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.
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).
The structure of liquids, glasses and other non-crystalline solids is characterized by the absence of long-range order which defines crystalline materials. Liquids and amorphous solids do, however, possess a rich and varied array of short to medium range order, which originates from chemical bonding and related interactions. Metallic glasses, for example, are typically well described by the dense random packing of hard spheres, whereas covalent systems, such as silicate glasses, have sparsely packed, strongly bound, tetrahedral network structures. These very different structures result in materials with very different physical properties and applications.
Artificial life is a field of study wherein researchers examine systems related to natural life, its processes, and its evolution, through the use of simulations with computer models, robotics, and biochemistry. The discipline was named by Christopher Langton, an American theoretical biologist, in 1986. In 1987 Langton organized the first conference on the field, in Los Alamos, New Mexico. There are three main kinds of alife, named for their approaches: soft, from software; hard, from hardware; and wet, from biochemistry. Artificial life researchers study traditional biology by trying to recreate aspects of biological phenomena.
Martini is a coarse-grained (CG) force field developed by Marrink and coworkers at the University of Groningen, initially developed in 2004 for molecular dynamics simulation of lipids, later (2007) extended to various other molecules. The force field applies a mapping of four heavy atoms to one CG interaction site and is parametrized with the aim of reproducing thermodynamic properties.
Charusita Chakravarty was an Indian academic and scientist. She was a professor of chemistry at the Indian Institute of Technology, Delhi since 1999. In 2009 she was conferred Shanti Swarup Bhatnagar Prize for Science and Technology in the field of chemical science. In 1999, she received B.M. Birla Science Award. She was an Associate Member of the Centre for Computational Material Science, Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore.
Bernd Michael Rode was an Austrian professor of chemistry at the University of Innsbruck and founder of the Austrian-South-East-Asian Academic University Network (ASEA-UNINET). Prof. Rode retired in 2011 but remained actively involved in teaching and research as well as in the thesis supervision.
Kurt Kremer is a German physicist.
Biman Bagchi is an Indian scientist currently serving as a SERB-DST National Science Chair Professor and Honorary Professor at the Solid State and Structural Chemistry Unit of the Indian Institute of Science. He is a theoretical physical chemist and biophysicist known for his research in the area of statistical mechanics; particularly in the study of phase transition and nucleation, solvation dynamics, mode-coupling theory of electrolyte transport, dynamics of biological macromolecules, protein folding, enzyme kinetics, supercooled liquids and protein hydration layer. He is an elected fellow of the Indian National Science Academy, the Indian Academy of Sciences, The World Academy of Sciences and an International honorary member of the American Academy of Arts and Sciences. Along with several scientific articles, he has authored three books, (i) Molecular Relaxation in Liquids, (ii) Water in Biological and Chemical Processes: From Structure and Dynamics to Function, and (iii) Statistical Mechanics for Chemistry and Materials Science.
Florian Müller-Plathe is a German theoretical chemist and professor for theoretical physical chemistry at Technische Universität Darmstadt.
Branka Maria Ladanyi was a physical chemist, who spent her career in the Department of Chemistry at Colorado State University. Her research focused on structure and dynamics of liquids, broadly defined, which she studied using theoretical and computational techniques.