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Better Partitions of Protein Graphs for Subsystem Quantum Chemistry
[chapter]
2016
Lecture Notes in Computer Science
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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
2014
Journal of magnetic resonance (San Diego, Calif. 1997 : Print)
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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
2018
Journal of Computational Chemistry
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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
2020
International Journal of Quantum Chemistry
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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
2014
Chemical Society Reviews
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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]
2019
arXiv
pre-print
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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
2020
Photochemistry and Photobiology
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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
2013
Journal of the Royal Society Interface
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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
2008
The international journal of high performance computing applications
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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
2006
Proteins: Structure, Function, and Bioinformatics
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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
2007
EurophysicsNews
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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
2012
Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences
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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]
2012
arXiv
pre-print
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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
2016
International Journal of Theoretical Physics
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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]
2021
arXiv
pre-print
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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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