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Common workflows for computing material properties using different quantum engines

npj Computational Materials 2021年第1期7卷 1202-1213页

作者： Sebastiaan P.Huber Emanuele Bosoni Marnik Bercx jens bröder Augustin Degomme Vladimir Dikan Kristjan Eimre Espen Flage-Larsen Alberto Garcia Luigi Genovese Dominik Gresch Conrad Johnston Guido Petretto Samuel Poncé Gian-Marco Rignanese Christopher J.Sewell Berend Smit Vasily Tseplyaev Martin Uhrin Daniel Wortmann Aliaksandr V.Yakutovich Austin Zadoks Pezhman Zarabadi-Poor Bonan Zhu Nicola Marzari Giovanni Pizzi Theory and Simulation of Materials(THEOS)and National Centre for Computational Design and Discovery of Novel Materials(MARVEL) École Polytechnique Fédérale de LausanneLausanneSwitzerland Institut de Ciència de Materials de Barcelona ICMAB-CSICBellaterraSpain Peter Grünberg Institut and Institute for Advanced Simulation Forschungszentrum JülichJülichGermany Department of Physics RWTH Aachen UniversityAachenGermany CEA IRIG-MEM-L_SimUniv.Grenoble-AlpesGrenobleFrance Nanotech@surfaces Laboratory Swiss Federal Laboratories for Materials Science and Technology(Empa)DübendorfSwitzerland SINTEF Industry Materials PhysicsOsloNorway Department of Physics University of OsloOsloNorway Microsoft Station Q University of CaliforniaSanta BarbaraCAUSA Atomistic Simulation Centre School of Mathematics and PhysicsQueen’s University BelfastBelfastUK UCLouvain Institut de la Matière Condensée et des Nanosciences(IMCN)Louvain-la-NeuveBelgium Laboratory of Molecular Simulation(LSMO) Institut des sciences et ingénierie chimiques(ISIC)École Polytechnique Fédérale de Lausanne(EPFL)ValaisSionSwitzerland Department of Chemistry Claverton DownUniversity of BathBathUK The Faraday Institution DidcotUK Department of Chemistry University College LondonLondonUK

The prediction of material properties based on density-functional theory has become routinely common,thanks,in part,to the steady increase in the number and robustness of available simulation *** plurality of codes and methods is both a boon and a *** providing great opportunities for cross-verification,these packages adopt different methods,algorithms,and paradigms,making it challenging to choose,master,and efficiently use *** demonstrate how developing common interfaces for workflows that automatically compute material properties greatly simplifies interoperability and *** introduce design rules for reusable,code-agnostic,workflow interfaces to compute well-defined material properties,which we implement for eleven quantum engines and use to compute various material *** implementation encodes carefully selected simulation parameters and workflow logic,making the implementer’s expertise of the quantum engine directly available to *** workflows are made available as open-source and full reproducibility of the workflows is guaranteed through the use of the AiiDA infrastructure.

关键词： quantum routine material

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Imaging of the gastrointestinal tract-novel technologies

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World Journal of Gastroenterology 2009年第2期15卷 160-168页

作者： jens brφndum Frφkjr Asbjφrn Mohr Drewes Hans Gregersen Mech-Sence Aalborg HospitalDK-9000 Aalborg Denmark Department of Radiology Aalborg Hospital DK-9000 Aalborg Denmark Mech-Sence Aalborg Hospital DK-9000 Aalborg Denmark Mech-Sense Department of Medical Gastroenterology Aalborg University Hospital DK-9000 Aalborg Denmark National Center for Ultrasound in Gastroenterology Haukeland University Hospital Bergen Norway Center for Sensory-Motor Interaction (SMI) Department of Health Science and Technology Aalborg University Denmark Center for Sensory-Motor Interaction (SMI) Department of Health Science and Technology Aalborg University DK-9000 Aalborg Denmark

Imaging of the gastrointestinal tract is very useful for research and clinical studies of patients with symptoms arising from the gastrointestinal tract and in visualising anatomy and pathology. Traditional radiological techniques played a leading role in such studies for a long time. However, advances in non-invasive modalities including ultrasound (US), computed tomography (CT), positron emission tomography (PET), magnetic resonance imaging (MRI), etc, have in the last decades revolutionised the way in which the gastrointestinal tract is studied. The resolution of imaging data is constantly being improved and 3D acquisition, tools for fi ltering, enhancement, segmentation and tissue classif ication are continually being developed. Additional co-registration techniques allow multimodal data acquisition with improved classif ication of tissue pathology. Furthermore, new functional imaging techniques have become available. Altogether, the future of gastrointestinal imaging looks very promising which will be of great benef it in clinical and research studies of gastrointestinal diseases. The purpose of this review is to highlight the capabilities of the newest techniques to explore the detailed morphology, biomechanical properties, function and pathology of the gastrointestinal tract.

关键词： Computed tomography Gastrointestinaltract Imaging Magnetic resonance Radiology Ultrasound

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Upper gastrointestinal sensory-motor dysfunction in diabetes mellitus

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World Journal of Gastroenterology 2006年第18期12卷 2846-2857页

作者： Jingbo Zhao jens brφndum Frφkjaer Asbjφrn Mohr Drewes Niels Ejskjaer Center of Excellence in Visceral Biomechanics and Pain Aalborg Hospital Sφndre Skovvej 15 DK-9000 Aalborg Denmark & Center for Sensory-Motor Interactions Department of Health Science Aalborg University Fredrik Bajers Vej 7 D-3 DK-9220 Aalborg Denmark Department of Medicine M (Diabetes & Endocrinology) Aarhus University Hospital Norrebrogade 44 DK 8000 Aarhus C Denmark

Gastrointestinal （GI） sensory-motor abnormalities are common in patients with diabetes mellitus and may involve any part of the GI tract. Abnormalities are frequently sub-clinical, and fortunately only rarely do severe and life-threatening problems occur. The pathogenesis of abnormal upper GI sensory-motor function in diabetes is incompletely understood and is most likely multi-factorial of origin. Diabetic autonomic neuropathy as well as acute suboptimal control of diabetes has been shown to impair GI motor and sensory function. Morphological and biomechanical remodeling of the GI wall develops during the duration of diabetes, and may contribute to motor and sensory dysfunction. In this review sensory and motility disorders of the upper GI tract in diabetes is discussed; and the morphological changes and biomechanical remodeling related to the sensory-motor dysfunction is also addressed.

关键词： Diabetes Esophagus Stomach Intestine Motility Pain Diabetic neuropathy Hyperglycemia Remodeling

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Morphological and functional evaluation of chronic pancreatitis with magnetic resonance imaging

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World Journal of Gastroenterology 2013年第42期19卷 7241-7246页

作者： Tine Maria Hansen Matias Nilsson Mikkel Gram jens brφndum Frφkjr Mech-Sense Department of RadiologyAalborg University Hospital9000 AalborgDenmark Mech-Sense Department of GastroenterologyAalborg University Hospital9000 AalborgDenmark

Magnetic resonance imaging(MRI)techniques for assessment of morphology and function of the pancreas have been improved dramatically the recent years and MRI is very often used in diagnosing and follow-up of chronic pancreatitis(CP)*** MRI including fat-suppressed T1-weighted and T2-weighted imaging techniques reveal decreased signal and glandular atrophy of the pancreas in *** contrast-enhanced MRI of the pancreas in CP the pancreatic signal is usually reduced and delayed due to decreased perfusion as a result of chronic inflammation and ***,morphological changes of the ductal system can be assessed by magnetic resonance cholangiopancreatography(MRCP).Furthermore,secretin-stimulated MRCP is a valuable technique to evaluate side branch pathology and the exocrine function of the pancreas and diffusion weighted imaging can be used to quantify both parenchymal fibrotic changes and the exocrine function of the *** standard and advanced MRI techniques are supplementary techniques to reveal morphological and functional changes of the pancreas in ***,spectroscopy has been used for assessment of metabolite concentrations in-vivo in different tissues and may have the potential to offer better tissue characterization of the ***,the purpose of the present review is to provide an update on standard and advanced MRI techniques of the pancreas in CP.

关键词： Magnetic resonance Chronic pancreatitis Secretin Diffusion weighted imaging Exocrine pancreatic function

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Systematic review of centrifugal valving based on digital twin modeling towards highly integrated lab-on-a-disc systems

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Microsystems & Nanoengineering 2021年第6期7卷 45-70页

作者： jens Ducrée School of Physical Sciences Dublin City UniversityDublinIreland

Current,application-driven trends towards larger-scale integration(LSI)of microfluidic systems for comprehensive assay automation and multiplexing pose significant technological and economical challenges to *** virtue of their intrinsic capability for powerful sample preparation,centrifugal systems have attracted significant interest in academia and business since the early *** review models common,rotationally controlled valving schemes at the heart of such“Lab-on-a-Disc”(LoaD)platforms to predict critical spin rates and reliability of flow control which mainly depend on geometries,location and liquid volumes to be processed,and their experimental *** absence of larger-scale manufacturing facilities during product development,the method presented here facilitates efficient simulation tools for virtual prototyping and characterization and algorithmic design optimization according to key performance *** virtual in silico approach thus significantly accelerates,de-risks and lowers costs along the critical advancement from idea,layout,fluidic testing,bioanalytical validation,and scale-up to commercial mass manufacture.

关键词： centrifugal advancement modeling

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Impact of the spindle number on the material transport and mixing during planetary roller melt granulation Author links open overlay panel

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Particuology 2024年第8期91卷 260-267页

作者： Tom Lang jens Bartsch Laboratory of Solids Process Engineering Department of Biochemical and Chemical EngineeringTU Dortmund University44227DortmundGermany

In comparison to the established twin-screw machines,the application of a planetary roller granulator for continuous operation of melt granulation is a promising alternative based on the unique process *** initial study focused on the material transport during processing as a key driver for the overall ***,the impact of direct process parameters on the residence time distribution was the main *** investigations are complemented in this study by considering the free processing volume,which is defined by the number of planetary spindles applied within a *** impact on the processing conditions is evaluated with respect to the process setting in terms of feed rate and rotation *** results highlight the potential of altering the underlying transport function in planetary roller melt granulation(PRMG)via the investigated direct process and equipment *** impact of the feed rate is lower in comparison,while a higher rotation speed as well as a higher free processing volume promote material ***,a normalization of the determined residence time distribution(RTD)model data was feasible with respect to the process settings and the number of applied planetary spindles in the processing *** demonstrates the key role of the free processing volume in the fundamental mechanisms of material transport and mixing during PRMG.

关键词： Continuous manufacturing Melt granulation Planetaryroller granulator Quality-by-Design Residence time Material mixing

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Nash and Stackelberg Differential Games

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Chinese Annals of Mathematics,Series B 2012年第3期33卷 317-332页

作者： Alain BENSOUSSAN jens FREHSE jens VOGELGESANG International Center for Decision and Risk Analysis School of ManagementUniversity of Texas-Dallas800 West Camptell RdSM30RichardsonTX 75050-3021USA Faculty of Business The Hong Kong Polytechnic University Department of Mathematics Institute of Applied MathematicsUniversity of BonnGermany PACM Princeton UniversityUSA HCM University of BonnGermany

A large class of stochastic differential games for several players is considered in this *** class includes Nash differential games as well as Stackelberg differential games.A mix is *** existence of feedback strategies under general conditions is *** limitations concern the functionals in which the state and the controls appear *** is also true for the state *** controls appear in a quadratic form for the payoff and linearly in the state *** most serious restriction is the dimension of the state equation,which cannot exceed *** reason comes from PDE(partial differential equations) techniques used in studying the system of Bellman equations obtained by Dynamic Programming *** the authors' previous work in 2002,there is not such a restriction,but there are serious restrictions on the structure of the Hamiltonians,which are violated in the applications dealt with in this article.

关键词： Stochastic games Bellman equation Nonlinear elliptic and parabolicequations Stochastic differential games Hamiltonians

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Impaired contractility and remodeling of the upper gastrointestinal tract in diabetes mellitus type-1

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World Journal of Gastroenterology 2007年第36期13卷 4881-4890页

作者： jens brΦndum FrΦkjΦr SΦren Due Andersen Niels EjskjΦr Peter Funch-jensen AsbjΦrn Mohr Drewes Hans Gregersen Center for Visceral Biomechanics and Pain Aalborg Hospital Aalborg Denmark Department of Radiology Aalborg Hospital Aalborg Denmark Department of Endocrinology M Aarhus University Hospital Aarhus Denmark Department of Surgical Gastroenterology L Aarhus University Hospital Aarhus Denmark Center for Sensory-Motor Interaction Department of Health Science and Technology Aalborg University Denmark Center for Sensory-Motor Interaction Department of Health Science and Technology Aalborg University Denmark National Center for Ultrasound in Gastro-enterology Haukeland University Hospital Bergen Norway

AIM: To investigate that both the neuronal function of the contractile system and structural apparatus of the gastrointestinal tract are affected in patients with longstanding diabetes and auto mic neuropathy. METHODS: The evoked esophageal and duodenal contractile activity to standardized bag distension was assessed using a specialized ultrasound-based probe. Twelve type-1 diabetic patients with autonomic neuropathy and severe gastrointestinal symptoms and 12 healthy controls were studied. The geometry and biomechanical parameters (strain, tension/stress, and stiffness) were assessed. RESULTS: The diabetic patients had increased frequency of distension-induced contractions (6.0 ± 0.6 vs 3.3 ± 0.5, P 0.14). CONCLUSION: The impaired contractile activity with an imbalance in the distension-induced contractions likely reflects neuronal abnormalities due to autonomic neuropathy. However, structural changes and remodeling of the gastrointestinal tract are also evident and may add to the neuronal changes. This may contribute to the pathophysiology of diabetic gut dysfunction and impact on future management of diabetic patients with gastrointestinal symptoms.

关键词： Diabetes Autonomic Neuropathy Bio- mechanics Contractility Ultrasound Esophagus Duodenum Deformation Stress

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Pain and chronic pancreatitis: A complex interplay of multiple mechanisms

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World Journal of Gastroenterology 2013年第42期19卷 7282-7291页

作者： Jakob Lykke Poulsen Sφren Schou Olesen Lasse Paludan Malver jens brφndum Frφkjr Asbjφrn Mohr Drewes Mech-Sense Department of Gastroenterology and HepatologyAalborg University HospitalDK-9000 AalborgDenmark Mech-Sense Department of RadiologyAalborg University HospitalDK-9000 AalborgDenmark Center for Sensory-Motor Interactions (SMI) Department of Health Science and TechnologyAalborg UniversityDK-9000 AalborgDenmark

Despite multiple theories on the pathogenesis of pain in chronic pancreatitis,no uniform and consistently successful treatment strategy exists and abdominal pain still remains the dominating symptom for most patients and a major challenge for *** theories focussed on a mechanical cause of pain related to anatomical changes and evidence of increased ductal and interstitial *** observations form the basis for surgical and endoscopic drainage procedures,but the outcome is variable and often *** underscores the fact that other factors must contribute to pathogenesis of pain,and has shifted the focus towards a more complex neurobiological understanding of pain *** other explanations for pain,experimental and human studies have provided evidence that pain perception at the peripheral level and central pain processing of the nociceptive information is altered in patients with chronic pancreatitis,and resembles that seen in neuropathic and chronic pain ***,pain due to e.g.,complications to the disease and adverse effects to treatment must not be overlooked as an additional source of *** review outlines the current theories on pain generation in chronic pancreatitis which is crucial in order to understand the complexity and limitations of current therapeutic ***,it may also serve as an inspiration for further research and development of methods that can evaluate the relative contribution and interplay of different pain mechanisms in the individual patients,before they are subjected to more or less empirical treatment.

关键词： Chronic pancreatitis Abdominal pain Pain mechanisms Neuropathy Sensitization

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Development of fungal cell factories for the production of secondary metabolites:Linking genomics and metabolism

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Synthetic and Systems Biotechnology 2017年第1期2卷 5-12页

作者： jens Christian Nielsen jens Nielsen Chalmers University of Technology Kemivagen 10Sweden

The genomic era has revolutionized research on secondary metabolites and bioinformatics methods have in recent years revived the antibiotic discovery process after decades with only few new active molecules being *** computational tools are driven by genomics and metabolomics analysis,and enables rapid identification of novel secondary *** translate this increased discovery rate into industrial exploitation,it is necessary to integrate secondary metabolite pathways in the metabolic engineering *** this review,we will describe the novel advances in discovery of secondary metabolites produced by filamentous fungi,highlight the utilization of genome-scale metabolic models(GEMs)in the design of fungal cell factories for the production of secondary metabolites and review strategies for optimizing secondary metabolite production through the construction of high yielding platform cell factories.

关键词： Secondary metabolism Fungi Biosynthetic gene clusters Genome mining Metabolic modeling Cell factories

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