Molecular Dynamics
Molecular Dynamics - Related Videos
13:58
Probing C84-embedded Si Substrate Using Scanning Probe Microscopy and Molecular Dynamics
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Cited by 1 •
2016
This paper reports the nanomaterial fabrication of a fullerene Si substrate inspected and verified by nanomeasurements and molecular dynamic simulation.
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).
02:20
Dynamic Equilibrium
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2020
A reversible chemical reaction represents a chemical process that proceeds in both forward (left to right) and reverse (right to left) directions. When the rates of the forward and reverse reactions are equal, the concentrations of the reactant and product species remain constant over time and the system is at equilibrium. A special double arrow is used to emphasize the reversible nature of the reaction. The relative concentrations of reactants and products in equilibrium systems vary greatly;...
10:18
Molecular Orbital (MO) Theory
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2023
Source: Tamara M. Powers, Department of Chemistry, Texas A&M University This protocol serves as a guide in the synthesis of two metal complexes featuring the ligand 1,1'-bis(diphenylphosphino)ferrocene (dppf): M(dppf)Cl2, where M = Ni or Pd. While both of these transition metal complexes are 4-coordinate, they exhibit different geometries at the metal center. Using molecular orbital (MO) theory in conjunction with 1H NMR and Evans method, we will determine the geometry of these two...
09:55
Molecular Cloning
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2023
Molecular cloning is a set of methods, which are used to insert recombinant DNA into a vector - a carrier of DNA molecules that will replicate recombinant DNA fragments in host organisms. The DNA fragment, which may be a gene, can be isolated from a prokaryotic or eukaryotic specimen. Following isolation of the fragment of interest, or insert, both the vector and insert must be cut with restriction enzymes and purified. The purified pieces are joined together though a technique called...
FAQs
The force field supplies the interaction rules used while integrating Newton’s equations of motion. Its treatment of molecular forces therefore shapes the calculated trajectory, including how proteins flex and how interacting partners behave. In immunology and infection studies, this physics-based description supports analysis of structural changes that may affect antibody-antigen recognition or protein-ligand binding.
Temperature and pressure define the physical conditions under which the simulated system evolves. Changing these conditions can influence the molecular behavior represented in the trajectory, including structural flexibility and interactions. Researchers specify them to examine molecular processes under defined environments and to interpret computational observations within clearly stated simulation conditions.
Transient conformations are short-lived structural states captured during a simulated trajectory. They can expose molecular arrangements that are difficult to observe directly, adding a dynamic perspective to structural analysis. In infection and immunity research, these fleeting states may help explain recognition mechanisms, interaction changes, or potential binding opportunities that are not apparent from a single structure.
A typical workflow defines the molecular system, selects a force field, establishes temperature and pressure conditions, and integrates Newton’s equations of motion to generate a trajectory. Researchers then examine the resulting molecular behavior, such as flexibility or interactions. This sequence connects physical assumptions and simulation conditions to interpretable structural and mechanistic observations.
Simulations can follow how antibody and antigen structures move and interact over time, rather than treating recognition as a fixed structural event. The resulting trajectory may reveal flexible regions or transient conformations associated with their interaction. These observations provide mechanistic context for experimental studies of immune recognition and can help explain how molecular structure contributes to binding.
The method is useful for examining pathogen protein dynamics, membrane interactions, and protein-ligand binding. By showing how these systems behave over time, simulations can identify structural features and interaction patterns relevant to infection mechanisms. Those insights may help researchers evaluate promising drug targets while complementing experiments that cannot directly resolve every molecular state.