scholarly journals Construction of model Hamiltonians for adiabatic quantum computation and its application to finding low-energy conformations of lattice protein models

2008 ◽  
Vol 78 (1) ◽  
Author(s):  
Alejandro Perdomo ◽  
Colin Truncik ◽  
Ivan Tubert-Brohman ◽  
Geordie Rose ◽  
Alán Aspuru-Guzik
Keyword(s):  
Quantum Computation ◽  
Low Energy ◽  
Adiabatic Quantum Computation ◽  
Protein Models ◽  
Lattice Protein Models ◽  
Low Energy Conformations ◽  
Model Hamiltonians

scholarly journals Finding low-energy conformations of lattice protein models by quantum annealing

2012 ◽  
Vol 2 (1) ◽  
Author(s):  
Alejandro Perdomo-Ortiz ◽  
Neil Dickson ◽  
Marshall Drew-Brook ◽  
Geordie Rose ◽  
Alán Aspuru-Guzik
Keyword(s):  
Low Energy ◽  
Quantum Annealing ◽  
Protein Models ◽  
Lattice Protein Models ◽  
Low Energy Conformations

STUDIES OF FINDING LOW ENERGY CONFIGURATIONS IN OFF-LATTICE PROTEIN MODELS

2006 ◽  
Vol 05 (03) ◽  
pp. 587-594 ◽  
Author(s):  
JINGFA LIU ◽  
WENQI HUANG
Keyword(s):  
Lower Energy ◽  
Gradient Descent ◽  
Energy Landscape ◽  
Three Dimensional ◽  
Ground States ◽  
Low Energy ◽  
Protein Models ◽  
Energy Configurations ◽  
Energy Landscape Paving ◽  
Lattice Protein Models

We studied two three-dimensional off-lattice protein models with two species of monomers, hydrophobic and hydrophilic. Low energy configurations in both models were optimized using the energy landscape paving (ELP) method and subsequent gradient descent. The numerical results show that the proposed methods are very promising for finding the ground states of proteins. For all sequences with lengths 13 ≤ n ≤ 55, the algorithm finds states with lower energy than previously proposed putative ground states.

scholarly journals THE STRUCTURE OF THE FREE ENERGY SURFACE OF COARSE-GRAINED OFF-LATTICE PROTEIN MODELS

2007 ◽  
Vol 18 (01) ◽  
pp. 99-106 ◽  
Author(s):  
ETHEM AKTÜRK ◽  
HANDAN ARKIN ◽  
TARIK ÇELİK
Keyword(s):  
Energy Surface ◽  
Energy Landscape ◽  
Low Energy ◽  
Coarse Grained ◽  
Free Energy Surface ◽  
Protein Model ◽  
Energy Part ◽  
Folding Pathways ◽  
Protein Models ◽  
Lattice Protein Models

We have performed multicanonical simulations of hydrophobic-hydrophilic heteropolymers with a simple effective, coarse-grained off-lattice model to study the structure and the topology of the energy surface. The multicanonical method samples the whole rugged energy landscape, in particular the low-energy part, and enables one to better understand the critical behaviors and visualize the folding pathways of the considered protein model.

scholarly journals Generation of elementary gates and Bell’s states using controlled adiabatic evolutions

2019 ◽  
Vol 17 (03) ◽  
pp. 1950020
Author(s):  
Abderrahim Benmachiche ◽  
Ali Sellami ◽  
Sherzod Turaev ◽  
Derradji Bahloul ◽  
Azeddine Messikh ◽  
...  
Keyword(s):  
Quantum Computation ◽  
Open Systems ◽  
Circuit Model ◽  
Quantum Gates ◽  
Single Quantum ◽  
New Model ◽  
Adiabatic Quantum Computation ◽  
Usual Quantum

Fundamental quantum gates can be implemented effectively using adiabatic quantum computation or circuit model. Recently, Hen combined the two approaches to introduce a new model called controlled adiabatic evolutions [I. Hen, Phys. Rev. A, 91(2) (2015) 022309]. This model was specifically designed to implement one and two-qubit controlled gates. Later, Santos extended Hen’s work to implement [Formula: see text]-qubit controlled gates [A. C. Santos and M. S. Sarandy, Sci. Rep., 5 (2015) 15775]. In this paper, we discuss the implementation of each of the usual quantum gates, as well as demonstrate the possibility of preparing Bell’s states using the controlled adiabatic evolutions approach. We conclude by presenting the fidelity results of implementing single quantum gates and Bell’s states in open systems.

scholarly journals Realization of a classical counterpart of a scalable design for adiabatic quantum computation

2007 ◽  
Vol 90 (2) ◽  
pp. 022501 ◽  
Author(s):  
V. Zakosarenko ◽  
N. Bondarenko ◽  
S. H. W. van der Ploeg ◽  
A. Izmalkov ◽  
S. Linzen ◽  
...  
Keyword(s):  
Quantum Computation ◽  
Classical Counterpart ◽  
Adiabatic Quantum Computation ◽  
Scalable Design

Spatial Structure of the Acth-(6-9)-PGP Molecule

2021 ◽  
Vol 43 (5) ◽  
pp. 500-500
Author(s):  
Namiq Akhmedov Namiq Akhmedov ◽  
Leyla Agayeva Leyla Agayeva ◽  
Gulnara Akverdieva Gulnara Akverdieva ◽  
Rena Abbasli and Larisa Ismailova Rena Abbasli and Larisa Ismailova
Keyword(s):  
Amino Acid ◽  
Spatial Structure ◽  
Main Chain ◽  
Low Energy ◽  
Dihedral Angles ◽  
Amino Acid Residues ◽  
Analysis Method ◽  
Theoretical Conformational Analysis ◽  
Energy Of Hydrogen Bonds ◽  
Low Energy Conformations

The spatial structure of ACTH-(6-9)-PGP molecule has been investigated using theoretical conformational analysis method. Amino acid sequence of the N-terminal pentapeptide fragment of His-Phe-Arg-Trp-Pro of this molecule conforms to the fragment 6-9 of ACTH hormone. Calculations of conformational states of this molecule are carried out regarding nonvalent, electrostatic and torsional interactions and the energy of hydrogen bonds. The spatial structure of the His-Phe-Arg-Trp-Pro-Gly-Pro molecule was estimated on the low–energy conformations of the N-terminal tetrapeptide fragment His-Phe-Arg-Trp and C-terminal tripeptide fragment Pro-Gly-Pro of this molecule. It is shown that the spatial structure of heptapeptide molecule can be presented by 11 low-energy forms of the main chain. The low–energy conformations of this molecule, the values of dihedral angles of the backbone and side chains of the amino acid residues were founded and the energies of intra- and inter-residual interactions were determined.

scholarly journals Enzyme-hydrolyzed Fruit of Jurinea mollis: A Rich Source of (-)-(8R,8′R)-Arctigenin

2016 ◽  
Vol 11 (10) ◽  
pp. 1934578X1601101 ◽  
Author(s):  
Rita Könye ◽  
Ágnes Evelin Ress ◽  
Anna Sólyomváry ◽  
Gergő Tóth ◽  
András Darcsi ◽  
...  
Keyword(s):  
Low Energy ◽  
Plant Tissues ◽  
Selective Isolation ◽  
Isolation Method ◽  
Specific Accumulation ◽  
Fruit Wall ◽  
Lignan Glycoside ◽  
Nmr Methods ◽  
First Time ◽  
Low Energy Conformations

In Jurinea mollis fruit, the dibenzylbutyrolactone-type lignan glycoside arctiin and its aglycone arctigenin were determined for the first time using a combination of optimized enzymatic treatment and complementary spectrometric (HPLC-MS, GC-MS) and spectroscopic (CD and NMR) methods. Analysis of separated fruit parts, i.e., the fruit wall and embryo, demonstrated the specific accumulation of arctiin, since it was exclusively found in the embryo. Arctiin in the embryo samples (71.5 mg/g) was found to be quantitatively converted into arctigenin (50.7 mg/g) by endogenous enzymatic hydrolysis, resulting in one of the highest arctigenin-containing plant tissues reported to date and allowing the selective isolation of arctigenin by our recently reported three-step isolation method. The absolute configuration of the isolated arctigenin was determined to be (-)-(8 R,8′ R). Conformational analysis of arctigenin was also performed, resulting in three major low energy conformations.

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