Search results for " computational"
showing 10 items of 661 documents
Reliable numerical solution of a class of nonlinear elliptic problems generated by the Poisson-Boltzmann equation
2020
We consider a class of nonlinear elliptic problems associated with models in biophysics, which are described by the Poisson-Boltzmann equation (PBE). We prove mathematical correctness of the problem, study a suitable class of approximations, and deduce guaranteed and fully computable bounds of approximation errors. The latter goal is achieved by means of the approach suggested in [S. Repin, A posteriori error estimation for variational problems with uniformly convex functionals. Math. Comp., 69:481-500, 2000] for convex variational problems. Moreover, we establish the error identity, which defines the error measure natural for the considered class of problems and show that it yields computa…
Time-dependent screening explains the ultrafast excitonic signal rise in 2D semiconductors
2020
We calculate the time evolution of the transient reflection signal in an MoS$_2$ monolayer on a SiO$_2$/Si substrate using first-principles out-of-equilibrium real-time methods. Our simulations provide a simple and intuitive physical picture for the delayed, yet ultrafast, evolution of the signal whose rise time depends on the excess energy of the pump laser: at laser energies above the A- and B-exciton, the pump pulse excites electrons and holes far away from the K valleys in the first Brillouin zone. Electron-phonon and hole-phonon scattering lead to a gradual relaxation of the carriers towards small $\textit{Active Excitonic Regions}$ around K, enhancing the dielectric screening. The acc…
New Bioactive Peptides from the Mediterranean Seagrass Posidonia oceanica (L.) Delile and Their Impact on Antimicrobial Activity and Apoptosis of Hum…
2023
The demand for new molecules to counter bacterial resistance to antibiotics and tumor cell resistance is increasingly pressing. The Mediterranean seagrass Posidonia oceanica is considered a promising source of new bioactive molecules. Polypeptide-enriched fractions of rhizomes and green leaves of the seagrass were tested against Gram-positive (e.g., Staphylococcus aureus, Enterococcus faecalis) and Gram-negative bacteria (e.g., Pseudomonas aeruginosa, Escherichia coli), as well as towards the yeast Candida albicans. The aforementioned extracts showed indicative MIC values, ranging from 1.61 μg/mL to 7.5 μg/mL, against the selected pathogens. Peptide fractions were further analyzed thr…
New Bioprecursor Prodrugs of Sulfadiazine: Synthesis, X-ray Structure and Hirshfeld Analysis
2022
Sulphonamide motif is found extensively in numerous chemotherapeutic drug candidates, it acts by stopping the production of folate inside the bacterial cell. Current research has established the synthesis and characterization of new bioprecursor prodrugs of sulfadiazine. The first prodrug, 3, was synthesized via the coupling of diazonium salt of sulfadiazine with ethyl acetoacetate in AcONa at 0 °C. The second prodrug, sulfadiazine-pyrazole, 5, was furnished via cyclocondensation of the hydrazono derivative, 3, and 2-pyridyl hydrazine, 4. The generated data from the X-ray analysis is interpreted and refined to obtain the crystal structure of the target compound, 5. Density functional th…
Theoretical and experimental studies of some main group compounds : from closed shell interactions to singlet diradicals and stable radicals
2012
Acquiring knowledge of different interactions within and between molecules is a fascinating undertaking as it not only deepens our understanding of chemical bonding but also offers insight into electronic structures, molecular properties and the connections between these two. This dissertation combines together three main group chemistry related topics within the aforementioned theme. Research presented in the first third of this dissertation describes wave function and density functional theory studies of weak inter- and intramolecular interactions in pnictogen-based dimers X3Pn···PnX3 (Pn = N-Bi; X = F-I), dithallenes RTlTlR (R = H, Me, tBu, Ph) and octachalcogen dications Ch82+ (Ch = S, …
Joining primal/dual subdivision surfaces
2012
International audience; In this article we study the problem of constructing an intermediate surface between two other surfaces defined by different iterative construction processes. This problem is formalised with Boundary Controlled Iterated Function System model. The formalism allows us to distinguish between subdivision of the topology and subdivision of the mesh. Although our method can be applied to surfaces with quadrangular topology subdivision, it can be used with any mesh subdivision (primal scheme, dual scheme or other.) Conditions that guarantee continuity of the intermediate surface determine the structure of subdivision matrices. Depending on the nature of the initial surfaces…
On the use of generalized harmonic means in image processing using multiresolution algorithms
2019
In this paper we design a family of cell-average nonlinear prediction operators that make use of the generalized harmonic means and we apply the resulting schemes to image processing. The new famil...
WITHDRAWN: An efficient multiscale algorithm
2016
The publisher regrets that this article has been temporarily removed. The reason for the overturn of the decision on ACHA-16-25 from Acceptance to Rejection is: One of the colleagues of the authors, Elisa Francomano, claims that the authors submitted the manuscript to ACHA without her knowledge and omitting her as one of the authors. The full Elsevier Policy on Article Withdrawal can be found at http://www.elsevier.com/locate/withdrawalpolicy .
Prediction of Disease–lncRNA Associations via Machine Learning and Big Data Approaches
2021
This chapter introduces long non-coding RNAs and their role in the occurrence and progress of diseases. The discovery of novel lncRNA-disease associations may provide valuable input to the understanding of disease mechanisms at the lncRNA level, as well as to the detection of biomarkers for disease diagnosis, treatment, prognosis, and prevention. Unfortunately, due to costs and time complexity, the number of possible disease-related lncRNAs verified by traditional biological experiments is very limited. Computational approaches for the prediction of potential disease-lncRNA associations can effectively decrease the time and cost of biological experiments. We first review the main computatio…
Efficient mesoscale hydrodynamics: Multiparticle collision dynamics with massively parallel GPU acceleration
2018
Abstract We present an efficient open-source implementation of the multiparticle collision dynamics (MPCD) algorithm that scales to run on hundreds of graphics processing units (GPUs). We especially focus on optimizations for modern GPU architectures and communication patterns between multiple GPUs. We show that a mixed-precision computing model can improve performance compared to a fully double-precision model while still providing good numerical accuracy. We report weak and strong scaling benchmarks of a reference MPCD solvent and a benchmark of a polymer solution with research-relevant interactions and system size. Our MPCD software enables simulations of mesoscale hydrodynamics at lengt…