Ab-initio Simulation
Ab-initio Simulation - Related Videos
06:37
Analyzing Melts and Fluids from Ab Initio Molecular Dynamics Simulations with the UMD Package
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Cited by 2 •
2021
Melts and fluids are ubiquitous vectors of mass transport in natural systems. We have developed an open-source package to analyze ab initio molecular-dynamics simulations of such systems. We compute structural (bonding, clusterization, chemical speciation), transport (diffusion, viscosity) and thermodynamic properties (vibrational spectrum).
12:11
Computation of Atmospheric Concentrations of Molecular Clusters from ab initio Thermochemistry
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Cited by 22 •
2020
The atmospheric concentrations of weakly bound molecular clusters can be computed from the thermochemical properties of low energy structures found through a multi-step configurational sampling methodology utilizing a genetic algorithm and semi-empirical and ab initio quantum chemistry.
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Cited by 10 •
2010
The crown region of different V3 loop sequences of the surface envelope glycoprotein (gp120) of HIV-1 can be structurally characterized in many cases by in silico folding of positions 10 to 22 of the loop using a state-of-the-art ab initio folding algorithm. Here we demonstrate the folding and evaluation of this region of the V3 loop from the R2 strain of HIV-1, a uniquely neutralization sensitive strain with puzzling functional properties.
10:27
Contrast-Matching Detergent in Small-Angle Neutron Scattering Experiments for Membrane Protein Structural Analysis and Ab Initio Modeling
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Cited by 2 •
2018
This protocol demonstrates how to obtain a low-resolution ab initio model and structural details of a detergent-solubilized membrane protein in solution using small-angle neutron scattering with contrast-matching of the detergent.
09:46
MPI CyberMotion Simulator: Implementation of a Novel Motion Simulator to Investigate Multisensory Path Integration in Three Dimensions
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Cited by 48 •
2012
An efficient way to gain insight into how humans navigate themselves in three dimensions is described. The method takes advantage of a motion simulator capable of moving observers in ways unattainable by traditional simulators. Results confirm that movement in the horizontal plane is underestimated, while vertical movement is overestimated.
FAQs
Basis sets provide a mathematical representation for electron behavior in a calculation. Their choice helps determine how the electronic structure is represented and therefore affects computed molecular or material properties. In practice, they connect the abstract quantum-mechanical treatment to predictions such as geometries, energies, spectra, and intermolecular interactions.
Ab-initio simulation can use Hartree–Fock, post-Hartree–Fock theory, or density functional theory because these are distinct ways of treating electronic structure within the overall quantum-mechanical calculation. The selected approach determines how electron behavior is approximated and which calculated properties can be examined, including energies, geometries, reaction pathways, or spectra.
The electronic structure calculation supplies the link between electron behavior and chemical observables. Changes in this calculated structure can be examined alongside molecular geometry, energy, reaction pathway, spectrum, or intermolecular interaction. This connection allows a study to interpret why a chemical system behaves as observed, rather than treating the measured property as an isolated number.
A chemistry workflow can begin by representing the system with a basis set and calculating its electronic structure. The resulting calculation can then be used to examine molecular geometry, energy, reaction pathways, spectra, or intermolecular interactions. Which output receives emphasis depends on the scientific question, allowing the framework to support structural analysis, reaction analysis, or comparison with experimental observations.
Researchers can apply these calculations when they need molecular-level information about a reaction. Predicted energies and reaction pathways support analysis of how a chemical system may change, while the electronic-structure results provide atomic-scale context for interpreting that behavior. This makes the approach useful for examining reactions computationally alongside broader experimental or theoretical investigations.
The ability to calculate molecular and material properties from electronic structure supports catalyst design and materials development. Researchers can examine predicted geometries, energies, spectra, or intermolecular interactions to connect atomic-scale arrangements with observable behavior. These outputs provide computational evidence for analyzing candidate chemical systems and understanding how their structure relates to intended performance.
Calculated properties can provide an electronic-level explanation for observations made in experiments. Predicted molecular geometries, energies, spectra, and intermolecular interactions offer several points of comparison with measured chemical behavior. Agreement or contrast between calculated and experimental information can therefore guide interpretation of a system's structure, reactivity, or other observable characteristics.