Ion-matter interactions by MD simulations making use of reactive force fields

control of the optical properties of nanoparticles by laser fields

در این پایان نامه، درهمتنیدگی بین یک سیستم نقطه کوانتومی دوگانه(مولکول نقطه کوانتومی) و میدان مورد مطالعه قرار گرفته است. از آنتروپی ون نیومن به عنوان ابزاری برای بررسی درهمتنیدگی بین اتم و میدان استفاده شده و تاثیر پارامترهای مختلف، نظیر تونل زنی(که توسط تغییر ولتاژ ایجاد می شود)، شدت میدان و نسبت دو گسیل خودبخودی بر رفتار درجه درهمتنیدگی سیستم بررسی شده اشت.با تغییر هر یک از این پارامترها، در...

Reactive force fields made simple.

Generating a reactive force field for a given chemical reaction is turned from a many-months project for experts into a task of a few hours for a non-specialist, by joining the newly developed quantum-mechanically derived force field (QMDFF) and Warshel's time-tested empirical valence bond (EVB) idea. Three first example applications demonstrate that this works not just for simple atom exchange...

Force fields for protein simulations.

Improved model of hydrated calcium ion for molecular dynamics simulations using classical biomolecular force fields.

Calcium ions (Ca(2+) ) play key roles in various fundamental biological processes such as cell signaling and brain function. Molecular dynamics (MD) simulations have been used to study such interactions, however, the accuracy of the Ca(2+) models provided by the standard MD force fields has not been rigorously tested. Here, we assess the performance of the Ca(2+) models from the most popular cl...

Force fields and molecular dynamics simulations

The objective of this review is to serve as an introductory guide for the non-expert to the exciting field of Molecular Dynamics (MD). MD simulations generate a phase space trajectory by integrating the classical equations of motion for a system of N particles. Here I review the basic concepts needed to understand the technique, what are the key elements to perform a simulation and which is the...