Guidelines for Reporting Molecular Dynamics Simulations in JCIM Publications

All matter is composed of atoms, the smallest individual units of elements. Each atom is made up of three subatomic particles: protons, neutrons, and electrons. Together, these three particles account for the mass and the charge of an atom.The History of Atomic TheoryThe first person to propose that everything on Earth is made up of tiny particles was the Greek philosopher Democritus, around 450 B.C. He used the term atomos, Greek for “indivisible,” from which the modern term “atom” is derived.

Molecules have characteristic shapes that are crucial for their function. The arrangement of various electron groups around the central atom dictates their molecular geometry. Electron pairs in the valence shell of a central atom will adopt an arrangement that minimizes repulsions between the electron pairs by maximizing the distance between them. The valence electrons form either bonding pairs, located primarily between bonded atoms, or lone pairs.Two regions of electron density in a diatomic...

Overview

The fluid mosaic model was first proposed as a visual representation of research observations. The model comprises the composition and dynamics of membranes and serves as a foundation for future membrane-related studies. The model depicts the structure of the plasma membrane with a variety of components, which include phospholipids, proteins, and carbohydrates. These integral molecules are loosely bound, defining the cell’s border and providing fluidity for optimal function.LipidsThe most...

Physical models representing molecular architectures of chemical compounds play essential roles in understanding chemistry. The use of molecular models makes it easier to visualize the structures and shapes of atoms and molecules.

The motion of molecules in a gas is random in magnitude and direction for individual molecules, but a gas of many molecules has a predictable distribution of molecular speeds. This predictable distribution of molecular speeds is known as the Maxwell-Boltzmann distribution. The distribution of molecular speeds in liquids is comparable to that of gases but not identical and can help to understand the phenomenon of the boiling and vapor pressure of a liquid. Consider that a molecule requires a...