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Crystal Structure Prediction via Oblivious Local Search [article]

Dmytro Antypov, Argyrios Deligkas, Vladimir Gusev, Matthew J. Rosseinsky, Paul G. Spirakis, Michail Theofilatos
2020 arXiv   pre-print
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

Dmytro Antypov, Argyrios Deligkas, Vladimir Gusev, Matthew J. Rosseinsky, Paul G. Spirakis, Michail Theofilatos, Domenico Cantone, Simone Faro
2020 Symposium on Experimental and Efficient Algorithms  
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]

Sourav Manna, Snehasish Nandy, Bitan Roy
2021 arXiv   pre-print
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

I. G. Gurtubay, B. Rousseau, A. Bergara
2010 Physical Review B  
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

Vincent Frappier, Rafael J. Najmanovich, Alexander Donald MacKerell
2014 PLoS Computational Biology  
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

S. Schwartz
2003 Genome Research  
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]

Vincent Frappier, Rafael Najmanovich
2013 bioRxiv   pre-print
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

David L. Abel, Jack T. Trevors
2006 Physics of Life Reviews  
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

Ghanshyam Pilania, Eric Weis, Ethan M. Walker, Robert D. Gilbertson, Ross E. Muenchausen, Evgenya I. Simakov
2018 Scientific Reports  
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

Christopher Sutton, Mario Boley, Luca M. Ghiringhelli, Matthias Rupp, Jilles Vreeken, Matthias Scheffler
2020 Nature Communications  
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

Sheik Amamuddy, Veldman, Manyumwa, Khairallah, Agajanian, Oluyemi, Verkhivker, Tastan Bishop
2020 International Journal of Molecular Sciences  
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]

Colin Ophus, Ashivni Shekhawat, Haider I Rasool, Alex Zettl
2015 arXiv   pre-print
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

Gerard Kian-Meng Goh, A. Keith Dunker, Vladimir N. Uversky
2015 Molecular Biosystems  
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]

John H. Reif
1998 Lecture Notes in Computer Science  
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]

Dimitrios Georgakopoulos, Rajiv Ranjan, Karan Mitra, Xiangmin Zhou
2012 arXiv   pre-print
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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