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Quantum techniques for studying equilibrium in reaction networks

J. C. Baez, B. Fong
2014 Journal of Complex Networks  
This is an example of "stochastic mechanics", where we take techniques from quantum mechanics and replace amplitudes by probabilities.  ...  with mass-action kinetics admits an equilibrium solution obeying a certain "complex balance" condition.  ...  Acknowledgements This work was done at the Centre for Quantum Technologies, Singapore, which supported BF with a summer internship.  ... 
doi:10.1093/comnet/cnu013 fatcat:4sc22lj2ujbjpc337hibht4hn4

Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: coupled motions and distal mutations

S. Hammes-Schiffer, J. B Watney
2006 Philosophical Transactions of the Royal Society of London. Biological Sciences  
Nuclear quantum effects such as zero point energy and hydrogen tunnelling are significant in these reactions and substantially decrease the free energy barrier.  ...  A network of coupled motions representing conformational changes along the collective reaction coordinate facilitates the hydride transfer reaction by decreasing the donor-acceptor distance and providing  ...  We thank Steve Benkovic for helpful discussions.  ... 
doi:10.1098/rstb.2006.1869 pmid:16873124 pmcid:PMC1647314 fatcat:lxz756w7ojgonezzmkj6jvwkb4

Local quantum uncertainty as a robust metric to characterize discord-like quantum correlations in subsets of the chromophores in photosynthetic light-harvesting complexes

M. Chávez-Huerta, F. Rojas
2020 Revista mexicana de física  
Implementation of the LQU approach allows us to characterize quantum correlations that had not been studied before, identify the most quantum correlated subsets of chromophores, and determine that, in  ...  The FMO complex sustains quantum coherence and quantum correlations between the electronic states of spatially separated pigment molecules as energy moves with nearly a 100% quantum efficiency to the reaction  ...  Acknowledgments Thanks to DGAPA-UNAM with proyect PAPPIT IN10571 for finantial support.  ... 
doi:10.31349/revmexfis.66.525 fatcat:mlfgqdgx3zf5jgozesoigmitsm

Stepping Out of Equilibrium: The Quest for Understanding the Role of Non-Equilibrium (Thermo-)Dynamics in Electronic and Electrochemical Processes

Waldemar Kaiser, Alessio Gagliardi
2020 Entropy  
We present a brief outline on recent progress and challenges in the study of non-equilibrium dynamics and thermodynamics using numerical Monte Carlo simulations.  ...  The aim of this special issue is to collect recent advances and novel techniques of Monte Carlo methods to study non-equilibrium electronic and electrochemical processes at the nanoscale.  ...  In particular, the analyses of the charge and exciton dynamics in molecular electronics, and the reaction dynamics in electrochemical reaction networks, with the help of Monte Carlo methods, are the scope  ... 
doi:10.3390/e22091013 pmid:33286782 fatcat:rmlb7aaipvblpm6t52dy2nf5gy

A Review of Kinetic Modeling Methodologies for Complex Processes

Luís P. de Oliveira, Damien Hudebine, Denis Guillaume, Jan J. Verstraete, J.F. Joly
2016 Oil & Gas Science and Technology  
In this paper, kinetic modeling techniques for complex chemical processes are reviewed.  ...  For these three obstacles, molecular reconstruction techniques, deterministic or stochastic network generation programs, and single-event micro-kinetics and/or linear free energy relationships have been  ...  He described a graphical method for determining the order of a reaction in kinetic studies, studied the influence of the solvent for reactions in solution, introduced the modern concept of chemical affinity  ... 
doi:10.2516/ogst/2016011 fatcat:sndqjmpynzhk7jqybqy5qisjp4

Impact of Enzyme Motion on Activity†

Sharon Hammes-Schiffer
2002 Biochemistry  
These applications have also led to the proposal of a network of coupled promoting motions in enzymatic reactions. These concepts have important implications for protein engineering and drug design.  ...  Experimental and theoretical data imply that enzyme motion plays an important role in enzymatic reactions.  ...  ACKNOWLEDGMENT I owe great thanks to James Watney, Salomon Billeter, Pratul Agarwal, and Kim Wong for stimulating discussions and creation of the figures.  ... 
doi:10.1021/bi0267137 pmid:12416977 fatcat:tycg67mwtjg6ha42yxfni6igbm

Quantum Techniques for Reaction Networks

John C. Baez
2018 Advances in Mathematical Physics  
While reaction networks are mainly studied by chemists, they are equivalent to Petri nets, which are used for similar purposes in computer science and biology.  ...  Reaction networks are a general formalism for describing collections of classical entities interacting in a random way.  ...  This work was done at the Centre of Quantum Technology, in Singapore, and the Mathematics Department of U. C. Riverside.  ... 
doi:10.1155/2018/7676309 fatcat:yy3qd7dysbee7lt6ql2sudws4i

Discovery of a Synthesis Method for a Difluoroglycine Derivative Based on a Path Generated by Quantum Chemical Calculations

Tsuyoshi Mita, Yu Harabuchi, Satoshi Maeda
2020 Chemical Science  
In 2013, Maeda et al. introduced 'quantum chemistry aided retrosynthetic analysis'...  ...  The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge.  ...  Mingoo Jin is greatly acknowledged for assistance with the X-ray crystallographic analysis. This work was financially supported by a Grant-in-Aid for Scientific Research (C) (No.  ... 
doi:10.1039/d0sc02089c fatcat:xxxv5fgywfbv5md5woegobma4y

Discovery of a Synthesis Method for a Difluoroglycine Derivative Based on a Path Generated by Quantum Chemical Calculations

Tsuyoshi Mita, Yu Harabuchi, Satoshi Maeda
2020 Chemical Science  
In 2013, Maeda et al. introduced 'quantum chemistry aided retrosynthetic analysis'...  ...  The systematic exploration of synthetic pathways to afford a desired product through quantum chemical calculations remains a considerable challenge.  ...  Acknowledgements Dr Mingoo Jin is greatly acknowledged for assistance with the Xray crystallographic analysis. This work was  ... 
doi:10.1039/d0sc02089c pmid:34094133 pmcid:PMC8159455 fatcat:dzundh5msvcxndfj5egnhc7lgy

Natural Light Harvesting Systems: Unraveling the quantum puzzles [article]

A. Thilagam
2014 arXiv   pre-print
reaction centers culminates in the conversion of solar to chemical energy.  ...  The high speeds of excitation propagation within a system of interwoven biomolecular network structures, is yet to be replicated in artificial light harvesting complexes.  ...  The rich dynamics inherent in non-Hermitian quantum dynamics remains to be fully exploited, especially in studies involving the non-equilibrium quantum dynamics of dissipative molecular systems.  ... 
arXiv:1310.7761v3 fatcat:tmfvsbybzfdvxkt4y44mqu67fa

The geometric universality of currents

V Y Chernyak, M Chertkov, N A Sinitsyn
2011 Journal of Statistical Mechanics: Theory and Experiment  
chains of reactions in bio-chemical networks.  ...  We discuss a non-equilibrium statistical system on a graph or network.  ...  This material is also based upon work supported in part by the National Science Foundation under CHE-0808910 at Wayne State U, and under EMT-0829945 and ECCS-0925618 at NMC.  ... 
doi:10.1088/1742-5468/2011/09/p09006 fatcat:fnge2gyfwfcjrd4yakuxuy4fry

Quantum Techniques for Reaction Networks [article]

John C. Baez
2017 arXiv   pre-print
While reaction networks are mainly studied by chemists, they are equivalent to Petri nets, which are used for similar purposes in computer science and biology.  ...  Reaction networks are a general formalism for describing collections of classical entities interacting in a random way.  ...  I thank John Rowlands and Blake Stacey for catching typos and other mistakes, and the anonymous referees for suggesting improvements.  ... 
arXiv:1306.3451v2 fatcat:jz5b2zr52vgolk4unegqcne7sa

The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus

Hans-Peter Klenk, Rebecca A. Clayton, Jean-Francois Tomb, Owen White, Karen E. Nelson, Karen A. Ketchum, Robert J. Dodson, Michelle Gwinn, Erin K. Hickey, Jeremy D. Peterson, Delwood L. Richardson, Anthony R. Kerlavage (+39 others)
1997 Nature  
Kumar for discussions. We also thank the Medical Research Council of  ...  There are four characteristic outcomes expected for such a hypercyclic network, depending on the relative efficiencies of the coupled catalytic and autocatalytic reactions 2 .  ...  The data in this table (in units of 10 −8 M min −1 ) are for reactions containing the three peptide fragments in the absence and presence of added replicators.  ... 
doi:10.1038/37052 pmid:9389475 fatcat:67kot2xdgbhwbaykijixjlzl5a

Page 3456 of Mathematical Reviews Vol. , Issue 2001E [page]

2001 Mathematical Reviews  
Some results are consis- tent with earlier known studies, such as an equilibrium value of the second moment for constant frequency and the divergence of the value for random frequency, in which limiting  ...  Summary: “A reaction kernel, K(j,k) = K(k, j), is studied, for which the Smoluchowski equations of aggregation ¢; = , erat K(k Dexei[be+1,; — 5k,j —5),;] can be solved.  ... 

Quantum Techniques for Stochastic Mechanics [article]

John C. Baez, Jacob Biamonte
2019 arXiv   pre-print
For example, there is a widely used and successful theory of "chemical reaction networks", which describes the interactions of molecules in a stochastic rather than quantum way.  ...  We use this analogy to present new proofs of two major results in the theory of chemical reaction networks: the deficiency zero theorem and the Anderson-Craciun-Kurtz theorem.  ...  Research Station held in June 2014, and for educating him about chemical reaction networks  ... 
arXiv:1209.3632v5 fatcat:bdpnpttxbzd4ljxwp324h3cawq
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