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Better Partitions of Protein Graphs for Subsystem Quantum Chemistry [chapter]

Moritz von Looz, Mario Wolter, Christoph R. Jacob, Henning Meyerhenke
2016 Lecture Notes in Computer Science  
None of the existing graph partitioning work can be directly used, though, due to the unique constraints in partitioning such protein graphs.  ...  For the special case of partitioning a protein along the main chain, we also present an efficient dynamic programming algorithm that yields provably optimal results.  ...  Conclusions Partitioning protein graphs for subsystem quantum-chemistry is a new problem with unique constraints which general-purpose graph partitioning algorithms were unable to handle.  ... 
doi:10.1007/978-3-319-38851-9_24 fatcat:km7zmu43xzfxzoioix3me7xlhi

Quantum mechanical NMR simulation algorithm for protein-size spin systems

Luke J. Edwards, D.V. Savostyanov, Z.T. Welderufael, Donghan Lee, Ilya Kuprov
2014 Journal of magnetic resonance (San Diego, Calif. 1997 : Print)  
Nuclear magnetic resonance spectroscopy is one of the few remaining areas of physical chemistry for which polynomially scaling simulation methods have not so far been available.  ...  In the examples provided, the resulting reduction in the quantum mechanical simulation time is by many orders of magnitude.  ...  Palmer for stimulating discussions.  ... 
doi:10.1016/j.jmr.2014.04.002 pmid:24792963 fatcat:ltzdsga2jfbqlm4d5vqx3fudgu

Automated error control in divide-and-conquer self-consistent field calculations

Masato Kobayashi, Toshikazu Fujimori, Tetsuya Taketsugu
2018 Journal of Computational Chemistry  
It was confirmed that the present method works satisfactorily in calculations of water clusters and proteins, although its performance was insufficient for the calculation of a delocalized graphene system  ...  Program"); MEXT "Priority Issue on Post-K computer" (Development of new fundamental technologies for high-efficiency energy creation, conversion/storage and use). 2 ABSTRACT: In linear-scaling divide-and-conquer  ...  Acknowledgment Some of the present calculations were performed using the computer facilities at Research Center for Computational Science, Okazaki, and at Research Institute for Information Technology,  ... 
doi:10.1002/jcc.25174 pmid:29399822 fatcat:wrtds4tx5jdunanrinxjztnzfq

Analysis of environment response effects on excitation energies within subsystem‐based time‐dependent density‐functional theory

Linus Scholz, Johannes Tölle, Johannes Neugebauer
2020 International Journal of Quantum Chemistry  
K E Y W O R D S density-based embedding, quantum chemistry, solvent response, subsystem DFT, subsystem TDDFT 1 | INTRODUCTION Subsystem time-dependent density-functional theory (sTDDFT) [1] in the formulation  ...  To this end, we utilize the recently proposed "exact" version of sTDDFT relying on projection-based embedding (PbE), which so far was applied only for the special case of two subsystems.  ...  ACKNOWLEDGMENTS The authors would like to thank Moritz Bensberg for helpful discussions.  ... 
doi:10.1002/qua.26213 fatcat:7qwzcargwfcajbmhafslfya22i

Learning from photobiology how to design molecular devices using a computer

S. Gozem, F. Melaccio, H. L. Luk, S. Rinaldi, M. Olivucci
2014 Chemical Society Reviews  
Learning how to model photo-responsive proteins may open the way to the design of lightpowered biomimetic molecular devices.  ...  Acknowledgements We are grateful to Alessio Valentini and Luis Manuel Frutos for discussion and for anticipating the results of Fig. 18  ...  The partitioning of the QM/MM model into the QM and MM subsections. The decision on how to partition the system is crucial.  ... 
doi:10.1039/c4cs00037d pmid:24811294 fatcat:fr3jv23qn5bexla4ihakannnoy

Self-Parametrizing System-Focused Atomistic Models [article]

Christoph Brunken, Markus Reiher
2019 arXiv   pre-print
Our approach may also be employed for the generation of system-focused electrostatic molecular mechanics embedding environments in a quantum mechanical molecular-mechanical hybrid model for arbitrary atomistic  ...  Computational studies of chemical reactions in complex environments such as proteins, nanostructures, or on surfaces require accurate and efficient atomistic models applicable to the nanometer scale.  ...  Acknowledgments The authors thank the Schweizerischer Nationalfonds for generous support (  ... 
arXiv:1908.10492v1 fatcat:jfuqnefjtfgyzm2jhyqjwmv4oe

Frontiers in Multiscale Modelling of Photoreceptor Proteins

Maria‐Andrea Mroginski, Suliman Adam, Gil S. Amoyal, Avishai Barnoy, Ana‐Nicoleta Bondar, Veniamin Borin, Jonathan R. Church, Tatiana Domratcheva, Bernd Ensing, Francesca Fanelli, Nicolas Ferré, Ofer Filiba (+27 others)
2020 Photochemistry and Photobiology  
This perspective article highlights the challenges in the theoretical description of photoreceptor proteins using multiscale modelling, as discussed at the CECAM workshop in Tel Aviv, Israel.  ...  The participants have identified grand challenges and discussed the development of new tools to address them.  ...  For photoreceptor proteins, the part treated using quantum chemistry would typically be chosen as the chromophoric part of the protein.  ... 
doi:10.1111/php.13372 pmid:33369749 pmcid:PMC9185909 fatcat:z47h22agyrb5lpgs6khakypc5i

Life as we know it

K. Friston
2013 Journal of the Royal Society Interface  
The existence of a Markov blanket means that internal states will appear to minimize a free energy functional of the states of their Markov blanket.  ...  This paper presents a heuristic proof (and simulations of a primordial soup) suggesting that life-or biological self-organization-is an inevitable and emergent property of any (ergodic) random dynamical  ...  I would like to thank two anonymous reviewers for their detailed and thoughtful help in presenting these ideas. The Wellcome Trust funded this work.  ... 
doi:10.1098/rsif.2013.0475 pmid:23825119 pmcid:PMC3730701 fatcat:skxkcgkterddpipf5p5bqdxivy

De Novo Ultrascale Atomistic Simulations On High-End Parallel Supercomputers

Aiichiro Nakano, Rajiv K. Kalia, Ken-ichi Nomura, Ashish Sharma, Priya Vashishta, Fuyuki Shimojo, Adri C. T. van Duin, William A. Goddard, Rupak Biswas, Deepak Srivastava, Lin H. Yang
2008 The international journal of high performance computing applications  
The EDC framework also enables adaptive hierarchical simulation with automated model transitioning assisted by graph-based event tracking.  ...  We present a de novo hierarchical simulation framework for first-principles based predictive simulations of materials and their validation on high-end parallel supercomputers and geographically distributed  ...  Branicio, and Cheng Zhang for their contribution on graph-based data mining.  ... 
doi:10.1177/1094342007085015 fatcat:tr2nbpzurjesje4jkoatsuecam

Mechanisms of guanosine triphosphate hydrolysis by Ras and Ras-GAP proteins as rationalized by ab initio QM/MM simulations

Bella L. Grigorenko, Alexander V. Nemukhin, Maria S. Shadrina, Igor A. Topol, Stanley K. Burt
2006 Proteins: Structure, Function, and Bioinformatics  
Conclusions of the modeling lead to a better understanding of the anticatalytic effect of cancer causing mutation of Gln61 from Ras, which has been debated in recent years. Proteins 2007;66: 456-466.  ...  The results of simulations are compared to the previous findings for the GTP hydrolysis in the Ras-GAP (p21 ras -p120 GAP ) protein complex.  ...  RESULTS Enzyme-Substrate (ES) Complex In pilot calculations, several partitioning schemes to the QM and MM subsystems were tested.  ... 
doi:10.1002/prot.21228 pmid:17094109 fatcat:rvjhctqtrrfkvh7wjoi4iy7ebq

Condensed matter theory by computer simulation: from materials to chemical biology features

Mauro Ferrario, Giovanni Ciccotti, Kurt Binder
2007 EurophysicsNews  
Giovanni Ciccotti is Professor of Structure of Matter at the University of Roma "La Sapienza". He has contributed to the development of Molecular Dynamics methods now for several decades.  ...  About the authors: Mauro Ferrario is Professor of Structure of Matter at the University of Modena. He is a computational physicist working on interdisciplinary problems between physics and chemistry.  ...  However, this program cannot be carried out straightforwardly: even dealing only with the associated electrons is still a challenge for the methods of quantum chemistry.  ... 
doi:10.1051/epn:2007009 fatcat:ej4xuto36bdb7nryzrpbzbsmdi

Decoherence in the chemical compass: the role of decoherence for avian magnetoreception

M. Tiersch, H. J. Briegel
2012 Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences  
We support this perspective by presenting an example system from spin chemistry, which is also of importance for biological systems, e.g. in avian magnetoreception.  ...  Contrary to the usual picture that decoherence destroys quantum properties and causes the quantum-to-classical transition, we argue that decoherence can also play a constructive role in driving quantum  ...  For entanglement to exist, coherences between subsystems are required, but the mere presence of coherences is not sufficient for subsystems to be entangled.  ... 
doi:10.1098/rsta.2011.0488 pmid:22908340 fatcat:2q2zqdg5nrcsjkygdws3ish3vu

Probabilistic and Flux Landscapes of the Phage λ Genetic Switch [article]

Nathan Borggren
2012 arXiv   pre-print
To this end, general integral forms for advection-diffusion equations have been developed and numerically solved for a variety of mutants and assumptions about the state of the cells.  ...  The low number of proteins and other sources of noise are non-negligble and corrections to the kinetics are essential to understanding the stability.  ...  to break this continuity sufficiently to warrant a new name and all of the residual mistake is entirely my own.  ... 
arXiv:1204.1953v1 fatcat:do4vjinaojadphxoe3vowb54oe

The 'Life Machine': A Quantum Metaphor for Living Matter

Mario Rasetti
2016 International Journal of Theoretical Physics  
Aim of this paper is to provide a scheme for the construction of a conceptual, virtual machine (the term has here a significance analogous to that of the Turing machine, i.e., a formal device which manipulates  ...  and evolves 'states'), able to perform all that living matter -as distinguished from inert matter -can do and inanimate matter cannot, in a setting consistent exclusively with the quantum laws.  ...  Acknowledgments Besides the legacy of the several unforgettable discussions with David, I wish to acknowledge the interminable exchanges of ideas of the past with Michael Conrad and Tullio Regge, both  ... 
doi:10.1007/s10773-016-3177-6 fatcat:3oxjjzpafra3xnb333aot6du74

Topological Properties and Characterizations [article]

John Hongguang Zhang
2021 arXiv   pre-print
There are three important types of structural properties that remain unchanged under the structural transformation of condensed matter physics and chemistry.  ...  The theories of molecular topology, topological quantum matter including topological insulators, topological metal and topological superconductors and topological quantum computing are reviewed.  ...  large subsystems in thermodynamics, the partition function is introduced to reveals the geometric characteristics of the fractal body [4] .  ... 
arXiv:2108.07061v1 fatcat:f4bntigmcnfsfjnaoaecgmgv6y
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