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https://www.readbyqxmd.com/read/29453094/a-multidisciplinary-study-of-3-%C3%AE-d-glucopyranosyl-5-substituted-1-2-4-triazole-derivatives-as-glycogen-phosphorylase-inhibitors-computation-synthesis-crystallography-and-kinetics-reveal-new-potent-inhibitors
#1
Sándor Kun, Jaida Begum, Efthimios Kyriakis, Evgenia C V Stamati, Thomas A Barkas, Eszter Szennyes, Éva Bokor, Katalin E Szabó, George A Stravodimos, Ádám Sipos, Tibor Docsa, Pál Gergely, Colin Moffatt, Myrto S Patraskaki, Maria C Kokolaki, Alkistis Gkerdi, Vassiliki T Skamnaki, Demetres D Leonidas, László Somsák, Joseph M Hayes
3-(β-d-Glucopyranosyl)-5-substituted-1,2,4-triazoles have been revealed as an effective scaffold for the development of potent glycogen phosphorylase (GP) inhibitors but with the potency very sensitive to the nature of the alkyl/aryl 5-substituent (Kun et al., Eur. J. Med. Chem. 2014, 76, 567). For a training set of these ligands, quantum mechanics-polarized ligand docking (QM-PLD) demonstrated good potential to identify larger differences in potencies (predictive index PI = 0.82) and potent inhibitors with K i 's < 10 μM (AU-ROC = 0...
February 2, 2018: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/29450422/remarkable-structural-effects-on-the-complexation-of-actinides-with-h-phosphonates-a-combined-experimental-and-quantum-chemical-study
#2
Aditi Chandrasekar, Brahmmananda Rao C V S, Mahesh Sundararajan, Tapan K Ghanty, N Sivaraman
The structural effects of the carbon chain on the extraction of actinides by organo-phosphorus extractants have been examined experimentally and by computation. Branched butyl H-phosphonates and their linear chain isomer, n-butyl H-phosphonate (DBHP), were synthesised and characterised using IR, NMR and GC-MS techniques. Their physical properties viz. viscosity, density and aqueous solubility have been examined. DBHP, Di-iso-butyl H phosphonate (DiBHP) and Di-sec-butyl H phosphonate (DsBHP) were employed for the extraction of uranium and americium ions from nitric acid...
February 16, 2018: Dalton Transactions: An International Journal of Inorganic Chemistry
https://www.readbyqxmd.com/read/29450414/first-principles-method-for-calculating-the-rate-constants-of-internal-conversion-and-intersystem-crossing-transitions
#3
R R Valiev, V N Cherepanov, G V Baryshnikov, D Sundholm
A method for calculating the rate constants for internal-conversion (k IC ) and intersystem-crossing (k ISC ) processes within the adiabatic and Franck-Condon (FC) approximations is proposed. The applicability of the method is demonstrated by calculation of k IC and k ISC for a set of organic and organometallic compounds with experimentally known spectroscopic properties. The studied molecules were pyrromethene-567 dye, psoralene, hetero[8]circulenes, free-base porphyrin, naphthalene, and larger polyacenes...
February 16, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29449597/substructure-activity-relationship-studies-on-antibody-recognition-for-phenylurea-compounds-using-competitive-immunoassay-and-computational-chemistry
#4
Fuyuan Zhang, Bing Liu, Guozhen Liu, Yan Zhang, Junping Wang, Shuo Wang
Based on the structural features of fluometuron, an immunizing hapten was synthesized and conjugated to bovine serum albumin as an immunogen to prepare a polyclonal antibody. However, the resultant antibody indicated cross-reactivity with 6 structurally similar phenylurea herbicides, with binding activities (expressed by IC 50 values) ranging from 1.67 µg/L to 42.71 µg/L. All 6 phenylurea herbicides contain a common moiety and three different substitutes. To understand how these three different chemical groups affect the antibody-phenylurea recognition activity, quantum chemistry, using density function theory (DFT) at the B3LYP/6-311++ G(d,p) level of theory, was employed to optimize all phenylurea structures, followed by determination of the 3D conformations of these molecules, pharmacophore analysis, and molecular electrostatic potential (ESP) analysis...
February 15, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29448404/lattice-wigner-equation
#5
S Solórzano, M Mendoza, S Succi, H J Herrmann
We present a numerical scheme to solve the Wigner equation, based on a lattice discretization of momentum space. The moments of the Wigner function are recovered exactly, up to the desired order given by the number of discrete momenta retained in the discretization, which also determines the accuracy of the method. The Wigner equation is equipped with an additional collision operator, designed in such a way as to ensure numerical stability without affecting the evolution of the relevant moments of the Wigner function...
January 2018: Physical Review. E
https://www.readbyqxmd.com/read/29448376/matrix-product-algorithm-for-stochastic-dynamics-on-networks-applied-to-nonequilibrium-glauber-dynamics
#6
Thomas Barthel, Caterina De Bacco, Silvio Franz
We introduce and apply an efficient method for the precise simulation of stochastic dynamical processes on locally treelike graphs. Networks with cycles are treated in the framework of the cavity method. Such models correspond, for example, to spin-glass systems, Boolean networks, neural networks, or other technological, biological, and social networks. Building upon ideas from quantum many-body theory, our approach is based on a matrix product approximation of the so-called edge messages-conditional probabilities of vertex variable trajectories...
January 2018: Physical Review. E
https://www.readbyqxmd.com/read/29448371/decoherence-approach-to-energy-transfer-and-work-done-by-slowly-driven-systems
#7
Wen-Ge Wang
A main problem, which is met when computing the energy transfer of or work done by a quantum system, comes from the fact that the system may lie in states with coherence in its energy eigenstates. As is well known, when the so-called environment-induced decoherence has happened with respect to a preferred basis given by the energy basis, no coherence exists among the energy basis and the energy change of the system can be computed in a definite way. I argue that one may make use of this property, in the search for an appropriate definition of quantum work for a total system that does not include any measuring apparatus...
January 2018: Physical Review. E
https://www.readbyqxmd.com/read/29447943/novel-mutant-of-escherichia-coli-asparaginase-ii-to-reduction-of-the-glutaminase-activity-in-treatment-of-acute-lymphocytic-leukemia-by-molecular-dynamics-simulations-and-qm-mm-studies
#8
Noeman Ardalan, Sako Mirzaie, Abbas Akhavan Sepahi, Ramazan Ali Khavari-Nejad
L-Asparaginases (ASNase) belong to a family of amidohydrolases, have both asparaginase and glutaminase activity. Acute lymphocytic leukemia (ALL) is an outrageous disease worldwide. Bacterial ASNase has been used for the treatment of ALL. Glutaminase activity of enzyme causes some side effect and it is not essential for anticancer activity. The aim of this study was engineering of Escherichia coli asparaginase II to find a mutant with reduced glutaminase activity by molecular docking, molecular dynamics (MD) and QM-MM (Quantum mechanics molecular dynamics) simulations...
March 2018: Medical Hypotheses
https://www.readbyqxmd.com/read/29447447/dl_mg-a-parallel-multigrid-poisson-and-poisson-boltzmann-solver-for-electronic-structure-calculations-in-vacuum-and-solution
#9
James C Womack, Lucian Anton, Jacek Dziedzic, Philip J Hasnip, Matthew Ian James Probert, Chris-Kriton Skylaris
The solution of the Poisson equation is a crucial step in electronic structure calculations, yielding the electrostatic potential-a key component of the quantum mechanical Hamiltonian. In recent decades, theoretical advances and increases in computer performance have made it possible to simulate the electronic structure of extended systems in complex environments. This requires the solution of more complicated variants of the Poisson equation, featuring nonhomogeneous dielectric permittivities, ionic concentrations with non-linear dependencies, and diverse boundary conditions...
February 15, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29444058/high-order-super-resolution-optical-fluctuation-imaging-based-on-low-pass-denoising
#10
Limin Zou, Su Zhang, Baokai Wang, Jiubin Tan
A new scheme of super-resolution optical fluctuation imaging (SOFI) is proposed to broaden its application in the high-order case by separating the elimination of shot noise from the computation of cumulant, applying the low-pass denoising (LPD) operator to SOFI. The high-order cumulants are derived from a basic recursion of moments with the suppression of shot noise by the LPD on raw data. SOFI based on LPD (LPD-SOFI) demonstrates a 10.6-fold lateral resolution enhancement with the cumulant order of the 16th and a seven-fold three-dimensional resolution enhancement with the cumulant order of the 10th in experiments performed on a sparse sample of quantum dots...
February 15, 2018: Optics Letters
https://www.readbyqxmd.com/read/29443962/a-programmable-two-qubit-quantum-processor-in-silicon
#11
T F Watson, S G J Philips, E Kawakami, D R Ward, P Scarlino, M Veldhorst, D E Savage, M G Lagally, Mark Friesen, S N Coppersmith, M A Eriksson, L M K Vandersypen
Now that it is possible to achieve measurement and control fidelities for individual quantum bits (qubits) above the threshold for fault tolerance, attention is moving towards the difficult task of scaling up the number of physical qubits to the large numbers that are needed for fault-tolerant quantum computing. In this context, quantum-dot-based spin qubits could have substantial advantages over other types of qubit owing to their potential for all-electrical operation and ability to be integrated at high density onto an industrial platform...
February 14, 2018: Nature
https://www.readbyqxmd.com/read/29443961/a-coherent-spin-photon-interface-in-silicon
#12
X Mi, M Benito, S Putz, D M Zajac, J M Taylor, Guido Burkard, J R Petta
Electron spins in silicon quantum dots are attractive systems for quantum computing owing to their long coherence times and the promise of rapid scaling of the number of dots in a system using semiconductor fabrication techniques. Although nearest-neighbour exchange coupling of two spins has been demonstrated, the interaction of spins via microwave-frequency photons could enable long-distance spin-spin coupling and connections between arbitrary pairs of qubits ('all-to-all' connectivity) in a spin-based quantum processor...
February 14, 2018: Nature
https://www.readbyqxmd.com/read/29440766/a-cnot-gate-between-multiphoton-qubits-encoded-in-two-cavities
#13
S Rosenblum, Y Y Gao, P Reinhold, C Wang, C J Axline, L Frunzio, S M Girvin, Liang Jiang, M Mirrahimi, M H Devoret, R J Schoelkopf
Entangling gates between qubits are a crucial component for performing algorithms in quantum computers. However, any quantum algorithm must ultimately operate on error-protected logical qubits encoded in high-dimensional systems. Typically, logical qubits are encoded in multiple two-level systems, but entangling gates operating on such qubits are highly complex and have not yet been demonstrated. Here we realize a controlled NOT (CNOT) gate between two multiphoton qubits in two microwave cavities. In this approach, we encode a qubit in the high-dimensional space of a single cavity mode, rather than in multiple two-level systems...
February 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/29439575/density-dependent-formulation-of-dispersion-repulsion-interactions-in-hybrid-qm-mm-models
#14
Carles Curutchet, Lorenzo Cupellini, Jacob Kongsted, Stefano Corni, Luca Frediani, Arnfinn Hykkerud Steindal, Ciro Achille Guido, Giovanni Scalmani, Benedetta Mennucci
Mixed QM/MM models are widely used to explore the structure, reactivity and electronic properties of complex chemical systems. Whereas such models typically include electrostatics, and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, non-electrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdWTS) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29439572/surface-hopping-dynamics-beyond-nonadiabatic-couplings-for-quantum-coherence
#15
Jong-Kwon Ha, In Seong Lee, Seung Kyu Min
Description of correct electron-nuclear couplings is crucial in modelling of nonadiabatic dynamics. Within traditional semiclassical or mixed quantum-classical dynamics, the coupling between quantum electronic states and classical nuclear trajectories is governed by nonadiabatic coupling vectors coupled to classical nuclear momenta. This enables us to develop a very powerful nonadiabatic dynamics algorithm, namely surface hopping dynamics, which can describe the splitting of nuclear wave packets and detailed balance...
February 13, 2018: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/29438834/two-site-jumps-in-dimethyl-sulfone-studied-by-one-and-two-dimensional-17-o-nmr-spectroscopy
#16
J Beerwerth, M Storek, D Greim, J Lueg, R Siegel, B Cetinkaya, W Hiller, H Zimmermann, J Senker, R Böhmer
Polycrystalline dimethyl sulfone is studied using central-transition oxygen-17 exchange NMR. The quadrupolar and chemical shift tensors are determined by combining quantum chemical calculations with line shape analyses of rigid-lattice spectra measured for stationary and rotating samples at several external magnetic fields. Quantum chemical computations predict that the largest principal axes of the chemical shift anisotropy and electrical field gradient tensors enclose an angle of about 73°. This prediction is successfully tested by comparison with absorption spectra recorded at three different external magnetic fields...
January 31, 2018: Journal of Magnetic Resonance
https://www.readbyqxmd.com/read/29438614/molecular-dynamics-simulations-with-quantum-mechanics-molecular-mechanics-and-adaptive-neural-networks
#17
Lin Shen, Weitao Yang
Direct molecular dynamics (MD) simulation with ab initio quantum mechanical and molecular mechanical (QM/MM) methods is very powerful for studying the mechanism of chemical reactions in complex environment but very time consuming. The computational cost on QM/MM calculations during MD simulations can be reduced significantly using semiempirical QM/MM methods with lower accuracy. To achieve higher accuracy at the ab initio QM/MM level, a correction on the existing semiempirical QM/MM model is an attractive way...
February 13, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29437454/post%C3%A2-hoc-verification-of-quantum-computation
#18
Joseph F Fitzsimons, Michal Hajdušek, Tomoyuki Morimae
We propose a set of protocols for verifying quantum computing at any time after the computation itself has been performed. We provide two constructions: one requires five entangled provers and a completely classical verifier; the other requires a single prover, a verifier, who is restricted to measuring qubits in the X or Z basis, and one-way quantum communication from the prover to the verifier. These results demonstrate that the verification can be achieved independently from the blindness. We also show that a constant round protocol with a single prover and a completely classical verifier is not possible, unless bounded error quantum polynomial time (BQP) is contained in the third level of the polynomial hierarchy...
January 26, 2018: Physical Review Letters
https://www.readbyqxmd.com/read/29435930/quantum-language-of-microrna-application-for-new-cancer-therapeutic-targets
#19
Yoichi Robertus Fujii
MicroRNA (miRNA) is the noncoding gene: therefore, the miRNA gene inheritably controls protein gene expression through transcriptional and post-transcriptional levels. Aberrant expression of miRNA genes causes various human diseases, especially cancers. Although cancer is a complex disease, cancer/miRNA implication has yet been grasped from the perspective of miRNA profile in bed side. Since miRNA is the mobile genetic element, the clinical verification of miRNA in microvesicle of blood is too much straggle to predict potential cancer/miRNA associations without bioinformatical computing...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29434508/quantum-machine-learning-a-classical-perspective
#20
REVIEW
Carlo Ciliberto, Mark Herbster, Alessandro Davide Ialongo, Massimiliano Pontil, Andrea Rocchetto, Simone Severini, Leonard Wossnig
Recently, increased computational power and data availability, as well as algorithmic advances, have led machine learning (ML) techniques to impressive results in regression, classification, data generation and reinforcement learning tasks. Despite these successes, the proximity to the physical limits of chip fabrication alongside the increasing size of datasets is motivating a growing number of researchers to explore the possibility of harnessing the power of quantum computation to speed up classical ML algorithms...
January 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
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