A5050392679- Advanced Optical Network Technologies
- Computational Drug Discovery Methods
- Software-Defined Networks and 5G
- SARS-CoV-2 and COVID-19 Research
- Epigenetics and DNA Methylation
- Optical Network Technologies
- Alzheimer's disease research and treatments
- Regional Development and Management Studies
- Nanopore and Nanochannel Transport Studies
- Protein Structure and Dynamics
- Network Traffic and Congestion Control
- Force Microscopy Techniques and Applications
- Vitamin C and Antioxidants Research
- Cholinesterase and Neurodegenerative Diseases
- Semiconductor Lasers and Optical Devices
- Complex Network Analysis Techniques
- Advanced Data Compression Techniques
- Plant Virus Research Studies
- Cloud Computing and Resource Management
- Recommender Systems and Techniques
- Photonic and Optical Devices
- Cancer-related gene regulation
- Lipid Membrane Structure and Behavior
- Mathematics, Computing, and Information Processing
- Microfluidic and Capillary Electrophoresis Applications
Max Planck Computing and Data Facility
2025
University of Rijeka
2012-2023
Heidelberg Institute for Theoretical Studies
2017-2019
Heidelberg University
2017
ABSTRACT We benchmarked the performance of GROMACS 2024 molecular dynamics (MD) code on a modern high‐performance computing (HPC) cluster with AMD CPUs up to 65,536 CPU cores. used five different MD systems, ranging in size from about 82,000 204 million atoms, and evaluated their using two Message Passing Interface (MPI) libraries, Intel‐MPI Open‐MPI. The largest system showed near‐perfect strong scaling 512 nodes or cores, maintaining parallel efficiency above 0.9 even at highest level...
The antioxidant activity and chemical stability of 6-amino-6-deoxy-L-ascorbic acid (D1) N-methyl-6-amino-6-deoxy-L-ascorbic (D2) were examined with ABTS DPPH assays compared the reference L-ascorbic (AA). In addition, optimal storing conditions, as well pH at which amino derivatives maintain stability, determined using mass spectrometry. Comparable activities observed for NH-bioisosteres AA. Moreover, D1 showed higher in an acidic medium than parent AA, D1, D2 share same docking profile,...
Background We use our earlier experimental studies of the catalytic mechanism DNA methyltransferases to prepare in silico a family novel mechanism-based inhibitors human Dnmt1. Highly specific methylation can be used for analysis epigenome and creation iPS cells. Results describe set adenosyl-1-methyl-pyrimidin-2-one derivatives as mammalian methyltransferase The have been designed bind simultaneously active site cofactor thus act transition-state analogues. Molecular dynamics showed that...
Significance: The majority of the drugs which target membrane-embedded protease γ-secretase show an unusual biphasic activation–inhibition dose-response in cells, model animals, and humans. Semagacestat avagacestat are two that can facilitate cognitive decline patients with Alzheimer’s disease. Initial mechanistic studies showed drugs, pathogenic mutations, produce same type changes activity. Results: DAPT, semagacestat LY-411,575, four different binding constants, a for amyloid-β-40...
The paper describes the design goals and methodology in creating a new model of optical telecommunication network. is implemented by discrete-event network simulator ns-3. advantages using existing core infrastructure provided ns-3 are analyzed compared to building own from scratch, or selecting tool among other simulators such as ns-2, OMNeT++, OPNET. requirements for feature functionality outlined high-level overview architecture its components provided. Finally, possibilities extending...
Network availability is of paramount importance in optical telecommunication networks. Their rising connectivity and consequently their compromised by link node failures, usually due to physical force (e.g. digging, earthquake or fire). Single failures can turn cause multiple case a failure hits shared risk group (SRLG), which logically distinct links sharing common resource, be it cable conduit. The number length SRLGs, as well the characteristics underlying topology significantly affect...
Network availability is an essential feature of optical telecommunication network. Should a failure network component occur, be it link or inside node, control plane must able to detect the and reroute traffic using spare components until repair done. Shared risk groups (SRLGs) are used describe situation where seemingly unrelated logical failures happen due single physical failure. For example, two more links might share bridge crossing; should happen, all them will damaged. Routing...
In optical networks a group of logically distinct links can unintentionally share physical resource (e.g, cable or duct). Such group, called shared risk link (SRLG), introduces situation where single failure common cause multiple failures. Failure usually occurs due to force digging earthquake) and causes failures links. Specifically, such both working spare wavelength path logical connection between two edge nodes fail at the same time, leaving them disconnected until repair is done. The...
Mechanical perturbations are ubiquitous in living cells, and many biological functions dependent on the mechanical response of lipid membranes. Recent force-spectroscopy studies have captured stepwise fracture stacks bilayers, avoiding substrate effects. However, effect stacking as well exact molecular mechanism process, is unknown. Here, we use atomistic coarse-grained force-clamp dynamics simulation to assess effects indentation stacked single bilayers. Our simulations show that rupture...
The available structures of viral proteins and RNA molecules related to SARS-CoV-2 are used screen design a new set drugs using the commercial databases molecular docking protocols. selected then studied further dynamics. Based on our earlier experiences we can target proteases, enzymes in DNA metabolism, protein-protein interactions. In this paper describe planned research development efforts for efficient screening drugs. Prior campaign, will develop open-source computational...
There have been several studies of natural compounds used as SARS-CoV-2 inhibitors. Among those, we selected the most viable anti-viral compound, rutin, a basis for structure-based molecular docking campaign using databases commercially available that are potential ligands. The known and well-studied main protease structure was target Asinex screening library filtered to select structurally similar pharmacokinetically feasible compounds. Before campaing, protein minimized were protonated...