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Crystal Structure Prediction via Oblivious Local Search
[article]
2020
arXiv
pre-print
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Secondly, we propose an oblivious algorithm for Crystal Structure Prediction that is based on local search. ...
We study Crystal Structure Prediction, one of the major problems in computational chemistry. ...
Can local search, or Axes neighborhood in particular, improve existing methods for crystal structure prediction by a simple integration as an intermediate step? ...
arXiv:2003.12442v1
fatcat:pesk4powkrfvja476hh4ljg44i
Crystal Structure Prediction via Oblivious Local Search
2020
Symposium on Experimental and Efficient Algorithms
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Secondly, we propose an oblivious algorithm for Crystal Structure Prediction that is based on local search. ...
We study Crystal Structure Prediction, one of the major problems in computational chemistry. ...
Structure Prediction via Oblivious Local Search (a) Unit cell. ...
doi:10.4230/lipics.sea.2020.21
dblp:conf/wea/AntypovDGRST20
fatcat:ngieb2qdfbelffepoysbl4yf4e
Higher-Order Topological Phases on Quantum Fractals
[article]
2021
arXiv
pre-print
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2022 accepted doi:10.1103/physrevb.105.l201301 arXiv:2109.03231v2 fatcat:4qdwyvdouvejtollx77556xsym
These predictions can be experimentally tested on designer electronic fractal materials, as well as on various highly tunable metamaterial platforms, such as photonic and acoustic lattices. ...
Here we theoretically show that a special class of crystalline, namely higher-order topological phases that via an extended bulk-boundary correspondence feature robust gapless modes on lower dimensional ...
Here, we focus only on the local or on site pairings which are oblivious to the underlying lattice structure, and thus possess natural immunity against the lack of crystalline order. ...
arXiv:2109.03231v1
fatcat:ghyqurkvpbb4hbrpkpm7vy4ukm
Undamped low-energy plasmon inAlH3at high pressure
2010
Physical Review B
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Pickard and Needs 16 predicted using densityfunctional theory ͑DFT͒ and a "random searching" technique a metallic phase of AlH 3 at 73 GPa with a structure of space group Pm3n. ...
In the absence of crystal local-field effects, which arise when the microscopic electric field varies rapidly over the unit cell, 24 the off-diagonal elements of the inverse dielectric matrix are negligible ...
doi:10.1103/physrevb.82.085113
fatcat:co4df3rforgermaltphphrpbp4
A Coarse-Grained Elastic Network Atom Contact Model and Its Use in the Simulation of Protein Dynamics and the Prediction of the Effect of Mutations
2014
PLoS Computational Biology
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Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. ...
We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. ...
) and GRASP (Groupe de Recherche Axé sur la Structure des Protéines). ...
doi:10.1371/journal.pcbi.1003569
pmid:24762569
pmcid:PMC3998880
fatcat:5m72pcof3vbqtpl2arsaq57mxm
Human-Mouse Alignments with BLASTZ
2003
Genome Research
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Many other classes of sequence analysis software benefit from availability of an experiment-based gold standard; protein alignments are checked against X-ray crystal structures and gene predictions are ...
Fortunately, we have sufficient local disk on each node to provide a copy of all the input that might be required. The output was stored via NFS in a central server. ...
doi:10.1101/gr.809403
pmid:12529312
pmcid:PMC430961
fatcat:rlkrhqpw6rdv5ke7zj7s3wwepu
A coarse-grained elastic network atom contact model and its use in the simulation of protein dynamics and the prediction of the effect of mutations
[article]
2013
bioRxiv
pre-print
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Normal mode analysis (NMA) methods are widely used to study dynamic aspects of protein structures. ...
We show that existing methods are biased towards the prediction of destabilizing mutations and that ENCoM is less biased at predicting stabilizing mutations. ...
We can predict the local changes in S 2 with ENCoM. ...
doi:10.1101/001495
fatcat:bzj4oowysjduxgevduff6ln6va
Self-organization vs. self-ordering events in life-origin models
2006
Physics of Life Reviews
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Crystallization and the spontaneously forming dissipative structures of Prigogine are examples of self-ordering. ...
"Self-organization" is without empirical and prediction-fulfilling support. No falsifiable theory of self-organization exists. ...
Amos used electron crystallography to study the structure of tubulin to predict structural interactions with nucleotides, drugs, motor proteins and microtubule-associated proteins [6] . ...
doi:10.1016/j.plrev.2006.07.003
fatcat:6bgxammhdnd4nmuodxg3futckq
Computational screening of organic polymer dielectrics for novel accelerator technologies
2018
Scientific Reports
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Within this technology, the choice of the dielectric material forming the accelerating structures, such as the photonic band gap (PBG) structures, is dictated by a range of interrelated factors including ...
The use of infrared lasers to power accelerating dielectric structures is a developing area of research. ...
The dielectric response computed herein, via employing the perfect polymeric models with all polymeric chains oriented along a particular crystal axis, corresponds to that of a perfect single crystal and ...
doi:10.1038/s41598-018-27572-1
pmid:29915267
pmcid:PMC6006378
fatcat:m4jciehnqzdxjjwj3wz5xgjud4
Identifying domains of applicability of machine learning models for materials science
2020
Nature Communications
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The utility of this approach is demonstrated by analyzing three state-of-the-art ML models for predicting the formation energy of transparent conducting oxides. ...
Python scripts for all computations involved in this research are available via the first authors GitHub account at https://github.com/csutton7/ML_domain_of_applicability. ...
Since this representation is oblivious to configurational disorder (i.e., many distinct structures that are possible at a given composition), it is expected to perform poorly across all space groups and ...
doi:10.1038/s41467-020-17112-9
pmid:32887879
fatcat:atctk6dpardltcpudtsjvmdkae
Integrated Computational Approaches and Tools for Allosteric Drug Discovery
2020
International Journal of Molecular Sciences
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Finally, before the structure can be used in the subsequent steps, one should validate the quality of the models via local and global metrics. ...
coupled residues in their local communities to propagate cooperative structural changes. ...
doi:10.3390/ijms21030847
pmid:32013012
pmcid:PMC7036869
fatcat:y2z5vnsylnduhc7gntjkpcoslq
Large-Scale Experimental and Theoretical Study of Graphene Grain Boundary Structures
[article]
2015
arXiv
pre-print
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We have characterized the structure of 176 different single-layer graphene grain boundaries using >1000 experimental HRTEM images using a semi-automated structure processing routine. ...
All experimental and simulated boundary structures are available online. ...
their local atomic structure as a function of misorientation angle. ...
arXiv:1508.00497v1
fatcat:dwnoipasqrbpbdjd2x7yxwcy2q
Shell disorder, immune evasion and transmission behaviors among human and animal retroviruses
2015
Molecular Biosystems
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Also NCBI-BLAST (Basic Local Alignment Search Tool) 28 was used to deternmine the presence of sequence alignment of RSV (Rous Sarcoma Virus) and HIV-1 nucleocapsid proteins. ...
Since then, many predictors that are more :"accurate" as assessed by CASP (Critical Assesment of Structure Prediction) 18 have been developed. ...
doi:10.1039/c5mb00277j
pmid:26080321
fatcat:7zdmp47ilndy3obdbx2ctkwm2y
Alternative Computational Models: A Comparison of Biomolecular and Quantum Computation
[chapter]
1998
Lecture Notes in Computer Science
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In addition to NP search problems and database search problems, we enumerate a wide variety of further potential practical applications of BMC and QC. ...
., NP search problems), if solved with polynomial time bounds, requires exponentially large volume for BMC, so BMC does not scale well to solve very large NP search problems. ...
search techniques for local and other combinatorial search problems), and in this case Grover's algorithm appears to require only volume logarithmic in the search space size N . ...
doi:10.1007/978-3-540-49382-2_10
fatcat:icfyjfvgejdznldkvarhgtdypm
MediaWise - Designing a Smart Media Cloud
[article]
2012
arXiv
pre-print
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The project develops a MediaWise Cloud platform that supports do-it-yourself creation, search, management, and consumption of multimedia content. ...
Concrete prediction or forecasting models must be built before the demands and behaviours of a CDN application can be predicted accurately. ...
These storage resources are different from the local storage (for example, the local hard drive) in each CPU resource (e.g., Amazon EC2 instance types), which is temporary or non-persistent and cannot ...
arXiv:1206.1943v2
fatcat:uqidkpkkajfq3nbtcl7cp7r6im
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