Search results for "theoretical"
showing 10 items of 11439 documents
Conformational Dynamics of the Dengue Virus Protease Revealed by Fluorescence Correlation and Single-Molecule FRET Studies.
2021
The dengue virus protease (DENV-PR) represents an attractive target for counteracting DENV infections. It is generally assumed that DENV-PR can exist in an open and a closed conformation and that active site directed ligands stabilize the closed state. While crystal structures of both the open and the closed conformation were successfully resolved, information about the prevalence of these conformations in solution remains elusive. Herein, we address the question of whether there is an equilibrium between different conformations in solution which can be influenced by addition of a competitive inhibitor. To this end, DENV-PR was statistically labeled by two dye molecules constituting a FRET …
Molecular Basis of SARS-CoV-2 Nsp1-Induced Immune Translational Shutdown as Revealed by All-Atom Simulations.
2021
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic represents the most severe global health crisis in modern human history. One of the major SARS-CoV-2 virulence factors is nonstructural protein 1 (Nsp1), which, outcompeting with the binding of host mRNA to the human ribosome, triggers a translation shutdown of the host immune system. Here, microsecond-long all-atom simulations of the C-terminal portion of the SARS-CoV-2/SARS-CoV Nsp1 in complex with the 40S ribosome disclose that SARS-CoV-2 Nsp1 has evolved from its SARS-CoV ortholog to more effectively hijack the ribosome by undergoing a critical switch of Q/E158 and E/Q159 residues that perfects Nsp1's interactions…
STAT1 and Its Crucial Role in the Control of Viral Infections
2022
The signal transducer and activator of transcription (STAT) 1 protein plays a key role in the immune response against viruses and other pathogens by transducing, in the nucleus, the signal from type I, type II and type III IFNs. STAT1 activates the transcription of hundreds of genes, some of which have been well characterized for their antiviral properties. STAT1 gene deletion in mice and complete STAT1 deficiency in humans both cause rapid death from severe infections. STAT1 plays a key role in the immunoglobulin class-switch recombination through the upregulation of T-bet; it also plays a key role in the production of T-bet+ memory B cells that contribute to tissue-resident humoral memory…
Volumes of aqueous block copolymers based on poly(propylene oxides) and poly(ethylene oxides) in a large temperature range: A quantitative description
2006
The focus of this paper was on a quantitative comprehension of temperature effect on the volumes of aqueous di-block and triblock copolymers, based on propylene oxide (PO) and ethylene oxide (EO) units. To this purpose, literature data dealing with (EO316PO94 + water) and (EO13PO30EO13 + water) mixtures were analyzed. The volume vs. temperature trends were rationalized on the basis of the (unimers + aggregate) equilibrium by taking into account the temperature effect on both the partial molar volumes of the unimeric and the aggregated copolymer as well as the equilibrium constant of micellization. The analysis extended to the expansibility allowed to quantify the contribution for the shift …
On the convergence of zero-point vibrational corrections to nuclear shieldings and shielding anisotropies towards the complete basis set limit in wat…
2016
The method and basis set dependence of zero-point vibrational corrections (ZPVCs) to nuclear magnetic resonance shielding constants and anisotropies has been investigated using water as a test system. A systematic comparison has been made using the Hartree–Fock, second-order Møller–Plesset perturbation theory (MP2), coupled cluster singles and doubles (CCSD), coupled cluster singles and doubles with perturbative triples corrections (CCSD(T)) and Kohn–Sham density functional theory with the B3LYP exchange-correlation functional methods in combination with the second-order vibrational perturbation theory (VPT2) approach for the vibrational corrections. As basis sets, the correlation consisten…
Few-body insights of multiquark exotic hadrons
2018
In this contribution we discuss the adequate treatment of the $4-$ and $5-$body dynamics within a constituent quark framework. We stress that the variational and Born-Oppenheimer approximations give energies rather close to the exact ones, while the diquark approximation might be rather misleading. Hall-Post inequalities provide very useful lower bounds that exclude possible stable states for some mass ratios and color wave functions.
Sparsity-aware multiple relay selection in large multi-hop decode-and-forward relay networks
2016
In this paper, we propose and investigate two novel techniques to perform multiple relay selection in large multi-hop decode-and-forward relay networks. The two proposed techniques exploit sparse signal recovery theory to select multiple relays using the orthogonal matching pursuit algorithm and outperform state-of-the-art techniques in terms of outage probability and computation complexity. To reduce the amount of collected channel state information (CSI), we propose a limited-feedback scheme where only a limited number of relays feedback their CSI. Furthermore, a detailed performance-complexity tradeoff investigation is conducted for the different studied techniques and verified by Monte …
Compression and load balancing for efficient sparse matrix-vector product on multicore processors and graphics processing units
2021
We contribute to the optimization of the sparse matrix-vector product by introducing a variant of the coordinate sparse matrix format that balances the workload distribution and compresses both the indexing arrays and the numerical information. Our approach is multi-platform, in the sense that the realizations for (general-purpose) multicore processors as well as graphics accelerators (GPUs) are built upon common principles, but differ in the implementation details, which are adapted to avoid thread divergence in the GPU case or maximize compression element-wise (i.e., for each matrix entry) for multicore architectures. Our evaluation on the two last generations of NVIDIA GPUs as well as In…
XPS structural data and correlation with Mossbauer spectra for Tin-organic compounds: adducts of RnSnCl4-n with 1,2-bis(diphenylphosphino)ethane
1982
Abstract Core level X-ray photoelectron spectra of 1:1 adducts of SnCl4 and RSnCl3 with DPE {[RnSnCl4−n} · DPE (n = 1, R = Me, Bun, Octn, Phn; n = 2, R = Ph; DPE = 1,2-bis(diphenylphosphino)ethane], have been measured in solid phase. The Sn3d 5 2 binding energies, corrected for the Madelung potential at the metal atom, are well correlated with both partial atomic charge on tin, accounting for relaxation upon ionization, and 119Sn Mossbauer isomer shifts. The results are discussed in terms of these molecular parameters.
Interplay between the Belousov-Zhabotinsky reaction-diffusion system and biomimetic matrices
2007
Abstract Interactions between reaction–diffusion systems and restricted host environments are a subject of widespread interest. In this work the behaviour of the Belousov–Zhabotinsky reaction was investigated in lamellar phases formed by phospholipid bilayers with relevance for biological systems. The influence of the reactive medium on the structure of the lipid matrix and, in turn, the influence of the matrix on the dynamical evolution of chemical patterns, were studied by small angle scattering.