MD Simulation of AEDG Peptide Complexes with New K2R Dendrimer and Dendrigraft

Biocompatible peptide dendrimers and dendrigrafts have useful properties for application in biomedicine. In previous papers the computational approach for study lysine dendrimers and dendrigrafts as well as their complexes with various medical peptides was used. In this paper the comparison of complex formation between molecules of therapeutic AEDG tetrapeptide and novel K2R peptide dendrimer or DG2 dendrigraft of near the same size and charge was fulfilled. The systems consisting of 16 therapeutic AEDG tetrapeptide molecules and one dendrimer or one dendrigraft were studied by molecular dynamics simulation. Full atomic models of these molecules in water with explicit counterions were used for this goal. First of all, the process of complex formation was studied. It was obtained that peptide molecules were attracted by both branched molecules and were quickly adsorbed by them. Times of complexes formation as well as size, anisotropy and structure of each complex were calculated. It was demonstrated that both K2R dendrimer and DG2 dendrigraft are effective for complexation of these peptide molecules but new dendrimer complex is more stable than dendrigraft complex because it has almost twice more hydrogen bonds with peptide molecules and 33% more ion pairs with their charged groups.

An Open Dynamical System Approach to Dissipative Quantum Dot Array Antennas

A new computational approach to quantum antennas based on first principle open stochastic quantum dynamics.<div><br></div><div>We develop a general computational approach for the analysis and design of quantum antenna systems comprised of coupled quantum dot arrays interacting with external fields and producing quantum radiation. The method is based on using the GKSL master equation to model quantum dissipation and decoherence. The density operator of a coupled two-level quantum dot (qbit) array, excited by classical external signals with variable amplitude and phase, is evolved in time using a quantum Liouville-like equation (the master equation). We illustrate the method in a numerical example where it is shown that manipulating the phase excitations of individual quantum dots may significantly enhance the directive radiation properties of the quantum dot antenna system<br></div>

An Open Dynamical System Approach to Dissipative Quantum Dot Array Antennas

A new computational approach to quantum antennas based on first principle open stochastic quantum dynamics.<div><br></div><div>We develop a general computational approach for the analysis and design of quantum antenna systems comprised of coupled quantum dot arrays interacting with external fields and producing quantum radiation. The method is based on using the GKSL master equation to model quantum dissipation and decoherence. The density operator of a coupled two-level quantum dot (qbit) array, excited by classical external signals with variable amplitude and phase, is evolved in time using a quantum Liouville-like equation (the master equation). We illustrate the method in a numerical example where it is shown that manipulating the phase excitations of individual quantum dots may significantly enhance the directive radiation properties of the quantum dot antenna system<br></div>

Computational Approach for the Fluid-Structure Interaction Design of Insect-Inspired Micro Flapping Wings

A flight device for insect-inspired flapping wing nano air vehicles (FWNAVs), which consists of the micro wings, the actuator, and the transmission, can use the fluid-structure interaction (FSI) to create the characteristic motions of the flapping wings. This design will be essential for further miniaturization of FWNAVs, since it will reduce the mechanical and electrical complexities of the flight device. Computational approaches will be necessary for this biomimetic concept because of the complexity of the FSI. Hence, in this study, a computational approach for the FSI design of insect-inspired micro flapping wings is proposed. This approach consists of a direct numerical modeling of the strongly coupled FSI, the dynamic similarity framework, and the design window (DW) search. The present numerical examples demonstrated that the dynamic similarity framework works well to make different two FSI systems with the strong coupling dynamically similar to each other, and this framework works as the guideline for the systematic investigation of the effect of characteristic parameters on the FSI system. Finally, an insect-inspired micro flapping wing with the 2.5-dimensional structure was designed using the proposed approach such that it can create the lift sufficient to support the weight of small insects. The existing area of satisfactory design solutions or the DW increases the fabricability of this wing using micromachining techniques based on the photolithography in the micro-electro-mechanical systems (MEMS) technology. Hence, the proposed approach will contribute to the further miniaturization of FWNAVs.

Using Machine Learning to Greatly Accelerate Path Integral Ab Initio Molecular Dynamics

Ab initio molecular dynamics (AIMD) has become one of the most popular and robust approaches for modeling complicated chemical, liquid, and material systems. However, the formidable computational cost often limits its widespread application in simulations of the largest scale systems. The situation becomes even more severe in cases where the hydrogen nuclei may be better described as quantized particles using a path integral representation. Here, we present a computational approach that combines machine learning with recent advances in path integral contraction schemes, and we achieve a two-orders-of-magnitude acceleration over direct path integral AIMD simulation while at the same time maintaining its accuracy.