Search results for "Simulation"

Cobalt complex based on cyclam for reversible binding of nitric oxide

2008

We report the synthesis and theoretical calculations of nitrosyl cobalt complexes based on saturated tetraazamacrocycle for the reversible binding of nitric oxide (NO). Density-functional theory provides a rigorous theoretical framework for analysing, interpreting and investigating important parameters in order to further tune the properties of these complexes to the target application. We focus on understanding the stability of complexes in methanol solution as well as their reactivity and stability evolution in the presence of NO, O2 and higher nitrogen oxides intermediates. Calculations have been used to explore appropriate combinations of different macrocycles, metal centres and ligands…

Experimental-Like Affinity Constants and Enantioselectivity Estimates from Flexible Docking

2012

Experimental-like affinity constants and enantioselectivity estimates, not predicted so far computationally, were obtained using a novel flexible modeling/docking combined strategy. The S- and R-warfarin-human serum albumin (HSA, site I) complexes were used as an interaction model. The process for a verified estimation includes the following: (i) ionized open chain forming at physiological pH (a recent focus); (ii) conformational search (molecular mechanics and Monte Carlo methods); (iii) rigid protein-flexible ligand docking (GlideXP) generating low energy paired S- and R-poses; (iv) graphical comparison against the X-ray crystal structure (unsatisfactory verification step); (v) quantum po…

How Fragile We Are: Influence of Stimulator of Interferon Genes (STING) Variants on Pathogen Recognition and Immune Response Efficiency.

2022

AbstractThe STimulator of INterferon Genes (STING) protein is a cornerstone of the human immune response. Its activation by cGAMP upon the presence of cytosolic DNA stimulates the production of type I interferons and inflammatory cytokines which are crucial for protecting cells from infections. STING signaling pathway can also influence both tumor-suppressive and tumor-promoting mechanisms, rendering it an appealing target for drug design. In the human population, several STING variants exist and exhibit dramatic differences in their activity, impacting the efficiency of the host defense against infections. Understanding the differential molecular mechanisms exhibited by these variants is o…

A High-Resolution Penalization Method for large Mach number Flows in the presence of Obstacles

2009

International audience; A penalization method is applied to model the interaction of large Mach number compressible flows with obstacles. A supplementary term is added to the compressible Navier-Stokes system, seeking to simulate the effect of the Brinkman-penalization technique used in incompressible flow simulations including obstacles. We present a computational study comparing numerical results obtained with this method to theoretical results and to simulations with Fluent software. Our work indicates that this technique can be very promising in applications to complex flows.

Special issue of Computers and Operations Research: GRASP with Path Relinking: Developments and applications

2013

A critical review on the implementation of static data sampling techniques to detect network attacks

2021

International audience; Given that the Internet traffic speed and volume are growing at a rapid pace, monitoring the network in a real-time manner has introduced several issues in terms of computing and storage capabilities. Fast processing of traffic data and early warnings on the detected attacks are required while maintaining a single pass over the traffic measurements. To palliate these problems, one can reduce the amount of traffic to be processed by using a sampling technique and detect the attacks based on the sampled traffic. Different parameters have an impact on the efficiency of this process, mainly, the applied sampling policy and sampling ratio. In this paper, we investigate th…

Exploring the SARS-CoV-2 Proteome in the Search of Potential Inhibitors via Structure-based Pharmacophore Modeling/Docking Approach

2020

To date, SARS-CoV-2 infectious disease, named COVID-19 by the World Health Organization (WHO) in February 2020, has caused millions of infections and hundreds of thousands of deaths. Despite the scientific community efforts, there are currently no approved therapies for treating this coronavirus infection. The process of new drug development is expensive and time-consuming, so that drug repurposing may be the ideal solution to fight the pandemic. In this paper, we selected the proteins encoded by SARS-CoV-2 and using homology modeling we identified the high-quality model of proteins. A structure-based pharmacophore modeling study was performed to identify the pharmacophore features for each…

On achieving intelligent traffic-aware consolidation of virtual machines in a data center using Learning Automata

2018

Unlike the computational mechanisms of the past many decades, that involved individual (extremely powerful) computers or clusters of machines, cloud computing (CC) is becoming increasingly pertinent and popular. Computing resources such as CPU and storage are becoming cheaper, and the servers themselves are becoming more powerful. This enables clouds to host more virtual machines (VMs). A natural consequence ofthis is that many modern-day data centers experience very high internaltraffic within the data centers themselves. This is, of course, due to the occurrence of servers that belong to the same tenant, communicating between themselves. The problem is accentuated when the VM deployment t…

Parameter identification for heterogeneous materials by optimal control approach with flux cost functionals

2021

The paper deals with the identification of material parameters characterizing components in heterogeneous geocomposites provided that the interfaces separating different materials are known. We use the optimal control approach with flux type cost functionals. Since solutions to the respective state problems are not regular, in general, the original cost functionals are expressed in terms of integrals over the computational domain using the Green formula. We prove the existence of solutions to the optimal control problem and establish convergence results for appropriately defined discretizations. The rest of the paper is devoted to computational aspects, in particular how to handle high sens…

A Language and Platform Independent Co-Simulation Framework Based on the Functional Mock-Up Interface

2019

The main goal of the Functional Mock-up Interface (FMI) standard is to allow the sharing of simulation models across tools. To accomplish this, FMI relies on a combination of XML-files and compiled C-code packaged in a zip archive. This archive is called a Functional Mock-up Unit (FMU). In theory, an FMU can support multiple platforms, but not necessarily in practice. Furthermore, software libraries for interacting with FMUs may not be available in a particular language or platform. Another issue is related to the protection of intellectual property (IP). While an FMU is free to only provide the C-code in its binary form, other resources within the FMU may be unprotected. Distributing model…