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https://www.readbyqxmd.com/read/28230915/a-singlet-oxygen-generating-agent-by-chirality-dependent-plasmonic-shell-satellite-nanoassembly
#1
Fengli Gao, Maozhong Sun, Wei Ma, Xiaoling Wu, Liqiang Liu, Hua Kuang, Chuanlai Xu
Photodynamic therapy (PDT) agent, which generates singlet oxygen ((1) O2 ) under light, has attracted significant attention for its broad biological and medical applications. Here, DNA-driven shell-satellite (SS) gold assemblies as chiral photosensitizers are first fabricated. The chiral plasmonic nanostructure, coupling with cysteine enantiomers on its surface, exhibits intense chiroplasmonic activities (-40.2 ± 2.6 mdeg) in the visible region. These chiral SS nanoassemblies have high reactive oxygen species generating efficiency under circular polarized light illumination, resulting in a (1) O2 quantum yield of 1...
February 23, 2017: Advanced Materials
https://www.readbyqxmd.com/read/28229340/theoretical-calculation-of-polarizability-isotope-effects
#2
Félix Moncada, Roberto Flores-Moreno, Andrés Reyes
We propose a scheme to estimate hydrogen isotope effects on molecular polarizabilities. This approach combines the any-particle molecular orbital method, in which both electrons and H/D nuclei are described as quantum waves, with the auxiliary density perturbation theory, to calculate analytically the polarizability tensor. We assess the performance of method by calculating the polarizability isotope effect for 20 molecules. A good correlation between theoretical and experimental data is found. Further analysis of the results reveals that the change in the polarizability of a X-H bond upon deuteration decreases as the electronegativity of X increases...
March 2017: Journal of Molecular Modeling
https://www.readbyqxmd.com/read/28229155/sulfate-radical-oxidation-of-aromatic-contaminants-a-detailed-assessment-of-density-functional-theory-and-high-level-quantum-chemical-methods
#3
Sangavi Pari, Inger A Wang, Haizhou Liu, Bryan M Wong
Advanced oxidation processes that utilize highly oxidative radicals are widely used in water reuse treatment. In recent years, the application of sulfate radical (SO4˙(-)) as a promising oxidant for water treatment has gained increasing attention. To understand the efficiency of SO4˙(-) in the degradation of organic contaminants in wastewater effluent, it is important to be able to predict the reaction kinetics of various SO4˙(-)-driven oxidation reactions. In this study, we utilize density functional theory (DFT) and high-level wavefunction-based methods (including computationally-intensive coupled cluster methods), to explore the activation energies of SO4˙(-)-driven oxidation reactions on a series of benzene-derived contaminants...
February 23, 2017: Environmental Science. Processes & Impacts
https://www.readbyqxmd.com/read/28228021/waiting-time-distribution-for-electron-transport-in-a-molecular-junction-with-electron-vibration-interaction
#4
Daniel S Kosov
On the elementary level, electronic current consists of individual electron tunnelling events that are separated by random time intervals. The waiting time distribution is a probability to observe the electron transfer in the detector electrode at time t+τ given that an electron was detected in the same electrode at an earlier time t. We study waiting time distribution for quantum transport in a vibrating molecular junction. By treating the electron-vibration interaction exactly and molecule-electrode coupling perturbatively, we obtain the master equation and compute the distribution of waiting times for electron transport...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28228018/the-dissociative-chemisorption-of-co2-on-ni-100-a-quantum-dynamics-study
#5
Azar Farjamnia, Bret Jackson
A quantum approach based on an expansion in vibrationally adiabatic eigenstates is used to explore the dissociative chemisorption of CO2 on Ni(100). The largest barrier to reaction corresponds to the formation of a bent anionic molecular precursor, bound to the surface by about 0.24 eV. The barrier to dissociation from this state is small. Our computed dissociative sticking probabilities on Ni(100) for molecules in the ground state are in very good agreement with available experimental data, reasonably reproducing the variation in reactivity with collision energy...
February 21, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28227414/breast-lesion-detection-and-characterization-with-3d-features
#6
Arathi Sreekumari, K S Shriram, Vivek Vaidya, Arathi Sreekumari, K S Shriram, Vivek Vaidya, Vivek Vaidya, K S Shriram, Arathi Sreekumari
Automated Breast Ultrasound (ABUS) is highly effective as breast cancer screening adjunct technology. Automation can greatly enhance the efficiency of the clinician sifting through the quantum of data in ABUS volumes to spot lesions. We have implemented a fully automatic generic algorithm pipeline for detection and characterization of lesions on such 3D volumes. We compare a wide range of features for region description on their effectiveness at the dual goals of lesion detection and characterization. On multiple feature images, we compute region descriptors at lesion candidate locations obviating the need for explicit lesion segmentation...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28226480/eeg-based-image-encryption-via-quantum-walks
#7
N Rawat, Y Shin, I Balasingham, N Rawat, Y Shin, I Balasingham, I Balasingham, N Rawat, Y Shin
An electroencephalogram (EEG) based image encryption combined with Quantum walks (QW) is encoded in Fresnel domain. The computational version of EEG randomizes the original plaintext whereas QW can serve as an excellent key generator due to its inherent nonlinear chaotic dynamic behavior. First, a spatially coherent monochromatic laser beam passes through an SLM, which introduces an arbitrary EEG phase-only mask. The modified beam is collected by a CCD. Further, the intensity is multiply with the QW digitally...
August 2016: Conference Proceedings: Annual International Conference of the IEEE Engineering in Medicine and Biology Society
https://www.readbyqxmd.com/read/28222598/drastic-compensation-of-the-electronic-and-solvation-effects-on-the-atp-hydrolysis-revealed-through-a-large-scale-qm-mm-simulations-combined-with-a-theory-of-solutions
#8
Hideaki Takahashi, Satoru Umino, Yuji Miki, Ryosuke Ishizuka, Shu Maeda, Akihiro Morita, Makoto Suzuki, Nobuyuki Matubayasi
Hydrolysis of adenosine triphosphate (ATP) is the "energy source" for a variety of biochemical processes. In the present work, we address key features of ATP hydrolysis: the relatively moderate value (about -10 kcal/mol) of the standard free energy ΔGhyd of reaction and the insensitivity of ΔGhyd to the number of excess electrons on ATP. We conducted quantum mechanical/molecular mechanical (QM/MM) simulation combined with the energy-representation theory of solutions to analyze the electronic-state and solvation contributions to ΔGhyd...
February 21, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28220854/prime-factorization-using-quantum-annealing-and-computational-algebraic-geometry
#9
Raouf Dridi, Hedayat Alghassi
We investigate prime factorization from two perspectives: quantum annealing and computational algebraic geometry, specifically Gröbner bases. We present a novel autonomous algorithm which combines the two approaches and leads to the factorization of all bi-primes up to just over 200000, the largest number factored to date using a quantum processor. We also explain how Gröbner bases can be used to reduce the degree of Hamiltonians.
February 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28220699/quantum-mechanical-study-on-the-catalytic-mechanism-of-alkaline-phosphatases
#10
Gabriela L Borosky
Alkaline phosphatases (APs) catalyze the hydrolysis and transphosphorylation of phosphate monoesters. The catalytic mechanism was examined by quantum-mechanical calculations using an active-site model based on the X-ray crystal structure of the human placental AP. Free energies of activation and of reaction for the catalytic steps were evaluated for a series of aryl and alkyl phosphate esters, and the computational results were compared with experimental values available in the literature. Mechanistic observations previously reported in experimental works were rationalized by the present theoretical study, particularly regarding the difference in the rate-determining step between aryl and alkyl phosphates...
February 21, 2017: Journal of Chemical Information and Modeling
https://www.readbyqxmd.com/read/28220440/quantum-probability-ranking-principle-for-ligand-based-virtual-screening
#11
Mohammed Mumtaz Al-Dabbagh, Naomie Salim, Mubarak Himmat, Ali Ahmed, Faisal Saeed
Chemical libraries contain thousands of compounds that need screening, which increases the need for computational methods that can rank or prioritize compounds. The tools of virtual screening are widely exploited to enhance the cost effectiveness of lead drug discovery programs by ranking chemical compounds databases in decreasing probability of biological activity based upon probability ranking principle (PRP). In this paper, we developed a novel ranking approach for molecular compounds inspired by quantum mechanics, called quantum probability ranking principle (QPRP)...
February 20, 2017: Journal of Computer-aided Molecular Design
https://www.readbyqxmd.com/read/28218316/theoretical-study-of-hcn-water-interaction-five-dimensional-potential-energy-surfaces
#12
Ernesto Quintas Sánchez, Marie-Lise Dubernet
A new five-dimensional potential energy surface is calculated at the coupled-cluster CCSD(T) level of theory for the HCN-water system, treating both monomers as rigid rotors. The associated methodology, which combines extensive ab initio calculations of moderate accuracy (CCSD(T)/AVDZ) and a fitting procedure involving a much lower angular coverage with more accurate ab initio calculations (CCSD(T)/CBS), is described in detail. This methodology provides a time-saving approach to compute quantitatively accurate potential energy surfaces with reasonable computational effort...
February 20, 2017: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/28217747/insights-into-photosystem-ii-from-isomorphous-difference-fourier-maps-of-femtosecond-x-ray-diffraction-data-and-quantum-mechanics-molecular-mechanics-structural-models
#13
REVIEW
Jimin Wang, Mikhail Askerka, Gary W Brudvig, Victor S Batista
Understanding structure-function relations in photosystem II (PSII) is important for the development of biomimetic photocatalytic systems. X-ray crystallography, computational modeling, and spectroscopy have played central roles in elucidating the structure and function of PSII. Recent breakthroughs in femtosecond X-ray crystallography offer the possibility of collecting diffraction data from the X-ray free electron laser (XFEL) before radiation damage of the sample, thereby overcoming the main challenge of conventional X-ray diffraction methods...
February 10, 2017: ACS Energy Lett
https://www.readbyqxmd.com/read/28217147/automatic-procedure-for-generating-symmetry-adapted-wavefunctions
#14
Marcus Johansson, Valera Veryazov
Automatic detection of point groups as well as symmetrisation of molecular geometry and wavefunctions are useful tools in computational quantum chemistry. Algorithms for developing these tools as well as an implementation are presented. The symmetry detection algorithm is a clustering algorithm for symmetry invariant properties, combined with logical deduction of possible symmetry elements using the geometry of sets of symmetrically equivalent atoms. An algorithm for determining the symmetry adapted linear combinations (SALCs) of atomic orbitals is also presented...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28216673/mechanistic-investigation-on-ros-resistance-of-phosphorothioated-dna
#15
Tingting Wu, Qiang Huang, Xiao-Lei Wang, Ting Shi, Linquan Bai, Jingdan Liang, Zhijun Wang, Zixin Deng, Yi-Lei Zhao
Phosphorothioated DNA (PT-DNA) exhibits a mild anti-oxidant property both in vivo and in vitro. It was found that 8-OHdG and ROS levels were significantly lower in dnd+ (i.e. S(+)) E. coli., compared to a dnd- (i.e. S(-)) strain. Furthermore, different from traditional antioxidants, phosphorothioate compound presents an unexpectedly high capacity to quench hydroxyl radical. Oxidative product analysis by liquid chromatography-mass spectrometry and quantum mechanistic computation supported its unique anti-oxidant characteristic of the hydroxyl selectivity: phosphorothioate donates an electron to either hydroxyl radical or guanine radical derived from hydroxyl radical, leading to a PS(•) radical; a complex of PS(•) radical and OH(-) (i...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28216652/universality-of-quantum-computation-with-cluster-states-and-x-y-plane-measurements
#16
Atul Mantri, Tommaso F Demarie, Joseph F Fitzsimons
Measurement-based quantum computing (MBQC) is a model of quantum computation where quantum information is coherently processed by means of projective measurements on highly entangled states. Following the introduction of MBQC, cluster states have been studied extensively both from the theoretical and experimental point of view. Indeed, the study of MBQC was catalysed by the realisation that cluster states are universal for MBQC with (X, Y)-plane and Z measurements. Here we examine the question of whether the requirement for Z measurements can be dropped while maintaining universality...
February 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28213950/benchmark-performance-of-global-switching-versus-local-switching-for-trajectory-surface-hopping-molecular-dynamic-simulation-cis-trans-azobenzene-photoisomerization
#17
Ling Yue, Le Yu, Chao Xu, Yibo Lei, Yajun Liu, Chaoyuan Zhu
Newly developed global switching algorithm that does not require calculation of nonadiabatic coupling vector reduces computational cost significantly. However, there is a lack of extensive checking its accuracy for this simplest nonadiabatic molecular dynamic method in comparison with conventional Tully's fewest switches. It is very necessary to demonstrate how accurate global switching algorithm is. Extensive comparison between local and global switching on-the-fly trajectory surface hopping molecular dynamics is performed for cis-to-trans (800 sampling trajectories) and trans-to-cis (600 sampling trajectories) azobenzene photoisomerization at the OM2/MRCI level...
February 18, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28211620/benchmark-ditopic-binding-of-cl-and-cs-by-the-macrocycle-hexacyclen
#18
Juan Ramon Aviles-Moreno, Giel Berden, Jos Oomens, Bruno Martinez-Haya
The ditopic binding of organic and inorganic anions and cations constitutes a distinct feature of polyazamacrocycles that underlies their action as intermediate docking and exchange ionophoric sites for tailored supramolecular synthesis and sensors. This work investigates the Cl- and Cs+ complexes formed by hexacyclen (1,4,7,10,13,16-hexaazacyclooctadecane, ha18c6), a benchmark building block of ion-pair polyamine receptors. Infrared action spectroscopy is employed to characterize the anionic and cationic complexes under controlled environmental conditions in an ion trap...
February 17, 2017: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
https://www.readbyqxmd.com/read/28211059/a-multipolar-approach-to-the-interatomic-covalent-interaction-energy
#19
Evelio Francisco, Daniel Menéndez Crespo, Aurora Costales, Ángel Martín Pendás
Interatomic exchange-correlation energies correspond to the covalent energetic contributions to an interatomic interaction in real space theories of the chemical bond, but their widespread use is severely limited due to their computationally intensive character. In the same way as the multipolar (mp) expansion is customary used in biomolecular modeling to approximate the classical Coulomb interaction between two charge densities ρA(r) and ρB(r), we examine in this work the mp approach to approximate the interatomic exchange-correlation (xc) energies of the Interacting Quantum Atoms method...
February 16, 2017: Journal of Computational Chemistry
https://www.readbyqxmd.com/read/28210878/the-role-of-weak-interactions-in-lignin-polymerization
#20
Ángel Sánchez-González, Francisco J Martín-Martínez, J A Dobado
Lignin is the most abundant natural polymer composed by aromatic moieties. Its chemical composition and its abundance have focused efforts to unlock its potential as a source of aromatic compounds for many years. The lack of a proper way for lignin de-polymerization has hampered its success as a natural solution for commodity aromatic chemicals, which is also due to the lack of understanding of the underlying mechanisms of lignin polymerization. A fuller fundamental understanding of polymerization mechanisms could lead to improvements in de-polymerization strategies, and therefore a proper methodology and a predictive theoretical framework are required for such purpose...
March 2017: Journal of Molecular Modeling
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