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  • 122201.
    Zolfaghari, Anahita
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.).
    Waldner, Carl-Johan
    KTH, School of Industrial Engineering and Management (ITM), Machine Design (Dept.).
    Bogramp till FRED 252010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Fred 25 is a boat that is supposed to be accessible to everyone, regardless of mobility. It is a 7.5 m long aluminum boat with ramp at the bow. The objective in the development of the boat has been that one wheelchair bound skipper can manage the boat all by himself. There are a number of problems with the boat to be resolved. In this project the focus has been on developing an inexpensive and effective sealing of the ramp and a locking of the ramp that goes to automate. These problems must be solved with minimal changes to the boat's current design. Developing the bow ramp with these requests is absolutely possible. However, it was difficult to obtain optimal solutions in which few or no changes could be made on the boat. This leads to solutions that counteract the built-in errors rather than erase them.For sealing the bottom of the ramp, the concept chosen consisted of a rubber mat that attaches to the outside of the ramp and the hull underneath the ramp.In order to seal the sides of the ramp a tubular rubber ledge was chosen. The rubber ledge clamps over the rib of the ramp and fills the gap between the ramp and the hull. The newly developed locking for the ramp follows the same principle as before i.e. a board with holes that folds over two locking bolts. Earlier this maneuver has been done manually, but with this new solution the board is hoisted up with the ramp and folds over the bolts automatically. Tests on the boat Fred 25 with the modifications which this project has resulted in has to be made for full evaluation.

  • 122202.
    Zolin Mooses, Jana
    KTH, School of Architecture and the Built Environment (ABE), Architecture.
    STÖDCENTER FÖR EU-IMMIGRANTER I LILJEHOLMEN2012Independent thesis Basic level (professional degree), 20 credits / 30 HE creditsStudent thesis
    Abstract [sv]

    STÖDCENTER FÖR EU-MIGRANTER I LILJEHOLMEN

    Idag består den snabbast växande gruppen hemlösa i Stockholm av arbetsimmigranter från andra EU-länder .

    Mitt projekt har som syfte att erbjuda denna grupp människor med en byggnad som kan hjälpa dem integreras in i samhället, och fungera som en länk och mellansteg mellan livet i utanförskap och ett värdigt liv med möjlighet till jobb, eget boende och social gemenskap.

  • 122203. Zoller, C. J.
    et al.
    Dentoni Litta, Eugenio
    KTH, School of Information and Communication Technology (ICT), Integrated Devices and Circuits.
    Primetzhofet, D.
    Characterization of high-k dielectrics using MeV elastic scattering of He ions2015In: Nuclear Instruments and Methods in Physics Research Section B: Beam Interactions with Materials and Atoms, ISSN 0168-583X, E-ISSN 1872-9584, Vol. 347, p. 52-57Article in journal (Refereed)
    Abstract [en]

    We present a systematic comparison of two distinct ion-beam based methods for composition analysis of nanometer oxide films: ion-beam channeling and elastic scattering using nuclear resonances, both at MeV energies. Thin films of the technologically highly relevant high-k dielectrics HfO2 and HfAIO are characterized in the present study, with the additional aim of obtaining a better quantification of the Al content for the latter system. We show that both employed ion scattering methods enable a quantitative determination of the oxygen concentrations with typical uncertainties of about 5-10% in the oxygen fraction. The influence of various kinds of systematic inaccuracies in the evaluation procedure are discussed.

  • 122204. Zolyomi, V.
    et al.
    Kollar, J.
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Anomalous surface relaxation in hcp transition metals2008In: Physical Review B. Condensed Matter and Materials Physics, ISSN 1098-0121, E-ISSN 1550-235X, Vol. 78, no 19Article in journal (Refereed)
    Abstract [en]

    First-principles total-energy calculations indicate anomalously large surface relaxations for groups IVA and VIIA hcp metals. In addition, for group VIIA elements the magnitude of the layer relaxation exhibits an unusually slow decay with the distance from the surface. We argue that the above phenomena can be traced back to the peculiar Fermi surface of groups IVA and VIIA hcp metals. Namely, the anomalous surface relaxation appears as a consequence of low-energy excitations with near 2k(F) wave vectors, which is also reflected by the flat and degenerate d bands located close to the Fermi level in the L-A-H plane of the hcp Brillouin zone.

  • 122205. Zolyomi, V.
    et al.
    Kollar, J.
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    On the surface relaxation of transition metals2008In: Philosophical Magazine, ISSN 1478-6435, E-ISSN 1478-6443, Vol. 88, no 18-20, p. 2709-2714Article in journal (Refereed)
    Abstract [en]

    First principles band structure calculations are presented for the layer relaxation of the close-packed surfaces of 5d transition metals. Anomalously large relaxations are found for group IVA and VIIA hcp metals. For these elements, the size of the layer relaxation exhibits an unusually slow decay with the distance from the surface. We argue that this phenomenon can be attributed to the peculiar flat and degenerate d-bands located close to the Fermi level in the L-A-H top-plane of the hcp Brillouin zone, and which are also responsible for the anomalously low [001] longitudinal optical phonon frequencies observed in these hcp metals.

  • 122206. Zolyomi, V.
    et al.
    Vitos, Levente
    KTH, School of Industrial Engineering and Management (ITM), Materials Science and Engineering, Applied Material Physics.
    Kwon, S. K.
    Kollar, J.
    Surface relaxation and stress for 5d transition metals2009In: Journal of Physics: Condensed Matter, ISSN 0953-8984, E-ISSN 1361-648X, Vol. 21, no 9Article in journal (Refereed)
    Abstract [en]

    Using the density functional theory, we present a systematic theoretical study of the layer relaxation and surface stress of 5d transition metals. Our calculations predict layer contractions for all surfaces, except for the ( 111) surface of face centered cubic Pt and Au, where slight expansions are obtained similarly to the case of the 4d series. We also find that the relaxations of the close packed surfaces decrease with increasing occupation number through the 5d series. The surface stress for the relaxed, most closely packed surfaces shows similar atomic number dependence as the surface energy. Using Cammarata's model and our calculated surface stress and surface energy values, we examine the possibility of surface reconstructions, which is in reasonable agreement with the experimental observations.

  • 122207.
    Zomer, Lara-Britt
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Transport Science.
    Daamen, Winnie
    TU Delft.
    Meijer, Sebastiaan
    KTH, School of Technology and Health (STH), Health Systems Engineering, Health Care Logistics.
    Hoogendoorn, Serge
    TU Delft.
    Managing Crowds: The Possibilities and Limitations of Crowd Information During Urban Mass Events2015Conference paper (Refereed)
    Abstract [en]

    Thischapter,basedonamixedmethodresearchapproach,offersinsights into possibilities and limitations of using ICT measures for crowd management and distribution during urban mass events (UMEs). Based on literature, practical applications and analyses of research results, we propose crowd management should consider characteristics of both crowds and UMEs to increase information effectiveness. In relation to urban planning, results show that possibilities to influence a crowd’s behavior depend on available (and known) choice sets offered in various locations, while distances towards locations across city centers appear less important. Limitations appear to be related to scarce knowledge on what drives crowd members to adapt or adhere to their activity choice behavior. Such insights are essential for smart cities striving for an optimal use of infrastructural capacity, as both the ambiguous effects of ICT measures, as well as a crowd’s self-organizing capacity should be taken into account for delaying, solving and preventing dis- ruptions of pedestrian flows in city centers. 

  • 122208.
    Zomer, Lara-Britt
    et al.
    KTH, School of Technology and Health (STH).
    Moustaid, Elhabib
    KTH, School of Technology and Health (STH).
    Meijer, Sebastiaan
    KTH, School of Technology and Health (STH).
    A META-MODEL FOR INCLUDING SOCIAL BEHAVIOR AND DATA INTO SMART CITY MANAGEMENT SIMULATIONS2015In: 2015 WINTER SIMULATION CONFERENCE (WSC), IEEE , 2015, p. 1705-1716Conference paper (Refereed)
    Abstract [en]

    Smart city management can be regarded to bridge different realms of thinking about cities, i.e. 1) the city as complex-adaptive system, 2) socio-technical operational control center and 3) multi-actor policy-making. Underpinned by different world views and theoretical bodies, integration of the three realms puts forward new demands on simulation approaches and challenges current knowledge and available technology regarding integration of sub-models across different systems. In order to support urban transportation management, a holistic approach is needed that semantically connects the three realms by incorporation of human behavior and knowledge. Combining research on knowledge management and computer science, this paper presents a novel meta-framework as socio-technical hybrid simulation language to generalize integration of simulations, gaming and data for modeling urban transportation.

  • 122209. Zomer, Lara-Britt
    et al.
    Moustaid, Elhabib
    KTH, School of Technology and Health (STH), Health Systems Engineering, Health Care Logistics.
    Meijer, Sebastiaan
    KTH, School of Technology and Health (STH), Health Systems Engineering, Health Care Logistics.
    A Meta-Model for Including Social Behavior and Data into Simulation in the Smart City Context2015In: Proceedings of the 2015 Winter Simulation Conference / [ed] L. Yilmaz, W. K. V. Chan, I. Moon, T. M. K. Roeder, C. Macal, and M. D. Rossetti, 2015Conference paper (Refereed)
    Abstract [en]

    mart city management can be regarded to bridge different realms of thinking about cities, i.e., 1) the city as complex-adaptive system, 2) socio-technical operational control center and 3) multi-actor policy-making. Underpinned by different world views and theoretical bodies, integration of the three realms puts forward new demands on simulation approaches and challenges current knowledge and available technology regarding integration of sub-models across different systems. In order to support urban transportation management, a holistic approach is needed that semantically connects the three realms by incorporation of human behavior and knowledge. Combining research on knowledge management and computer science, this paper presents a novel meta-framework as socio-technical hybrid simulation language to generalize integration of simulations, gaming and data for modeling urban transportation.

  • 122210.
    Zong, Jianing
    et al.
    KTH, School of Industrial Engineering and Management (ITM), Production Engineering.
    Shi, Yi
    KTH, School of Industrial Engineering and Management (ITM), Production Engineering.
    Kartläggning av databehov inom Scania Motortillverkning2018Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    The manufacturing industry is undergoing a transformation into a digital era. Industry 4.0 comprises digitization and connection of all aspects of its value chain, which results in more data being available and collected. The purpose of this degree project is to investigate the benefits that digitalization can bring to Scania’s engine manufacturing, with focus on improving the current KPIs (Key Performance Indicator). The following questions were formulated to ensure that this purpose could be reached:

    • How can Scania’s engine manufacturing improve KPIs in machining processes by collecting and analyzing data from machines?o What factors affect Scania’s current KPIs?

    o Which of the factors has the potential to develop further or control through the implementation of digitization?

    o Which machine data needs to be collected in order to improve KPIs and how can this data be collected?

    To answer these questions and investigate which data can be of use, a primarily qualitative method was initiated during the project. Information was collected from various aspects involved in production. This was done through observations, interviews and study visits. A quantitative study has also been performed to improve the generalizability of the thesis, by sorting and analyzing the existing collected data in the production line of the connecting rod.

    By combining literature studies with internal information gathering, the authors could further define the focus area to OPE (Overall Production Effectiveness), which is significant for productivity, and often does not reach the target value for Scania. Through an analysis of the data gathering from PUS (Production Follow-up System), factors that had a negative impact on OPE could be identified. The authors could also produce many concrete parameters by utilizing results from interviews of various functions within Scania. The parameters can be divided into three categories, Machine data, Tool data and Process data. A technical scan of tool and machine supplier has also been conducted to specify what data is possible to collect with the existing technology.

    The result of this degree project creates a starting point for digitalization of Scania’s engine manufacturing, which also results in potential new investments. According to the estimation of the authors, these investments will prove to be profitable on many levels over time.

  • 122211. Zong, N. C.
    et al.
    Li, H.
    Lam, M. P. Y.
    Jimenez, R. C.
    Kim, C. S.
    Deng, N.
    Kim, A. K.
    Choi, J. H.
    Zelaya, I.
    Liem, D.
    Meyer, D.
    Odeberg, Jacob
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Fang, C.
    Lu, H. -J
    Xu, T.
    Weiss, J.
    Duan, H.
    Uhlén, Mathias
    KTH, School of Biotechnology (BIO), Proteomics and Nanobiotechnology. KTH, Centres, Science for Life Laboratory, SciLifeLab.
    Yates III, J. R.
    Apweiler, R.
    Ge, J.
    Hermjakob, H.
    Ping, P.
    Integration of cardiac proteome biology and medicine by a specialized knowledgebase2013In: Circulation Research, ISSN 0009-7330, E-ISSN 1524-4571, Vol. 113, no 9, p. 1043-1053Article in journal (Refereed)
    Abstract [en]

    Rationale: Omics sciences enable a systems-level perspective in characterizing cardiovascular biology. Integration of diverse proteomics data via a computational strategy will catalyze the assembly of contextualized knowledge, foster discoveries through multidisciplinary investigations, and minimize unnecessary redundancy in research efforts. Objective: The goal of this project is to develop a consolidated cardiac proteome knowledgebase with novel bioinformatics pipeline and Web portals, thereby serving as a new resource to advance cardiovascular biology and medicine. Methods and results: We created Cardiac Organellar Protein Atlas Knowledgebase (COPaKB; www.HeartProteome.org), a centralized platform of high-quality cardiac proteomic data, bioinformatics tools, and relevant cardiovascular phenotypes. Currently, COPaKB features 8 organellar modules, comprising 4203 LC-MS/MS experiments from human, mouse, drosophila, and Caenorhabditis elegans, as well as expression images of 10 924 proteins in human myocardium. In addition, the Java-coded bioinformatics tools provided by COPaKB enable cardiovascular investigators in all disciplines to retrieve and analyze pertinent organellar protein properties of interest. Conclusions: COPaKB provides an innovative and interactive resource that connects research interests with the new biological discoveries in protein sciences. With an array of intuitive tools in this unified Web server, nonproteomics investigators can conveniently collaborate with proteomics specialists to dissect the molecular signatures of cardiovascular phenotypes.

  • 122212. Zong, Xu
    et al.
    Na, Yong
    Wen, Fuyu
    Ma, Guijun
    Yang, Jinhui
    Wang, Donge
    Ma, Yi
    Wang, Mei
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Li, Can
    Visible light driven H-2 production in molecular systems employing colloidal MoS2 nanoparticles as catalyst2009In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 30, p. 4536-4538Article in journal (Refereed)
    Abstract [en]

    Colloidal MoS2 nanoparticles with diameters of less than 10 nm were prepared with a simple solvothermal method and demonstrated high efficiency in catalyzing H-2 evolution in Ru(bpy)(3)(2+)-based molecular systems under visible light.

  • 122213.
    Zorbas, Dimitros
    et al.
    University of Piraeus.
    Douligeris, Christos
    University of Piraeus.
    Fodor, Viktoria
    KTH, School of Electrical Engineering (EES), Communication Networks. KTH, School of Electrical Engineering (EES), Centres, ACCESS Linnaeus Centre.
    Target location based sink positioning in wireless sensor networks2011In: 2011 18th International Conference on Telecommunications, ICT 2011, 2011, p. 21-26Conference paper (Refereed)
    Abstract [en]

    One of the main challenges in wireless sensor networks is to prolong the network lifetime by efficiently handling the limited battery life of the nodes. This problem becomes harder in applications where the nodes are randomly dropped in the field. In this paper we deal with the problem of the sink placement and of the network longevity, assuming a number of points in the field with known positions which must be covered by the sensors. Unlike other approaches, we consider the more realistic scenario where the coordinates of the sensors are not assumed to be known in advance and, thus, they cannot be used for the computation of the positions of the sinks. We present two solutions for the above problem; one based on the distance between the points and the second on the probability that a sensor may cover many points. We evaluate our approaches and compare them to algorithms that use the knowledge of the positions of the sensors in order to compute likely sink locations. It is shown that both proposed approaches present similar or better performance concerning network lifetime, while at the same time they significantly decrease the algorithm complexity.

  • 122214.
    Zorita, Julio
    KTH, School of Electrical Engineering (EES), Space and Plasma Physics.
    Dynamics of small satellites with gravity gradient attitude control2011Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    SWIM (Space Weather using Ion Spectrometers and Magnetometers) is a CubeSat to be launched with the purpose of studying interaction between the Sun and the Earth. A magnetometer will be placed in a boom which provides gravity gradient stabilization. SWIM will be inserted in a 600 km circular orbit and it is required to maintain a LVLH (Local Vertical Local Horizontal) position. This master thesis analyses the dynamical behavior of SWIM. For doing so an attitude simulator and a mass model have been developed. Mass model has been designed according to linear stability analysis. Simulations with the mass model have been carried out from the most ideal environment to realistic orbit. As a result it has been deduced that gravity gradient stabilization propagates initial conditions which are perturbed by aerodynamic and magnetic torques. Magnetic torques could lead to uncontrolled yaw spin. Additionally the deployment of two solar panels to guarantee passive stabilization for yaw axes has been studied. Three axes stabilization and LVLH pointing can be achieved in an orbit lower than 600 km.

  • 122215. Zorn, Anna-Marie
    et al.
    Malkoch, Michael
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Carlmark Malkoch, Anna
    KTH, School of Chemical Science and Engineering (CHE), Fibre and Polymer Technology.
    Barner-Kowollik, Christopher
    High temperature synthesis of vinyl terminated polymers based on dendronized acrylates: a detailed product analysis study2011In: POLYMER CHEMISTRY, ISSN 1759-9954, Vol. 2, no 5, p. 1163-1173Article in journal (Refereed)
    Abstract [en]

    The combination of dendrons and high temperature acrylate polymerization represents a viable route to form dendronized macromonomers. Dendronized acrylates based on 2,2-bis(hydroxymethyl) propionic acid (bis-MPA) were synthesized using dendrimer synthesis and click chemistry (copper catalyzed azide alkyne cycloaddition (CuAAC)). The synthesis was carried out up to the 3rd generation and with a carbon spacer length of 6 or 9 between the acrylic function and the dendron core. These dendronized acrylates were subjected to auto-initiated high temperature acrylate polymerization. The polymerization was performed at 140 degrees C in a 5 wt% solution of hexyl acetate with a 2,2'-azobis(isobutyronitrile) (AIBN) concentration of 5 x 10(-3) g mol(-1). The vinyl terminated polymers were in-depth characterized via size exclusion chromatography (SEC) and size exclusion chromatography coupled to electrospray ionization mass spectrometry (SEC-ESI-MS) to assess the generated product spectrum and the efficiency of the process. The achievable number average molecular weight, M-n, was between 1700 and 4400 g mol(-1). The degree of polymerization, DPn, decreases with increasing generations of the dendronized acrylates from 6.3 to 3.4. The purity of vinyl terminated oligomers containing a geminal double bond is up to 83%, with the dendronized acrylates of the 1st generation providing the best result. Moderate deprotection of the acetonide groups occurred spontaneously during the macromonomer formation process and reached its maximum at generation 3.

  • 122216. Zou, Bin
    et al.
    Li, Zong-Liang
    Song, Xiu-Neng
    Luo, Yi
    KTH, School of Biotechnology (BIO), Theoretical Chemistry.
    Wang, Chuan-Kui
    Effects of field-induced geometry relaxation on the electron transport properties of 4,4'-biphenyldithiol molecular junction2007In: Chemical Physics Letters, ISSN 0009-2614, E-ISSN 1873-4448, Vol. 447, no 03-jan, p. 69-73Article in journal (Refereed)
    Abstract [en]

    The non-linear charge transport properties of 4,4 '-biphenyldithiol molecular junction have been studied using the generalized Green's function theory. It is shown that the torsion angle between two phenyls is slightly decreased as increase of the external voltage while the whole molecule moves slightly along the reversed direction of the electric field. Calculations indicate that the inclusion of molecular geometry relaxation can avoid a false prediction of negative differential resistance behavior. The charge redistribution under the external bias results in resistive dipoles inside the molecule. The calculated I-V curves of 4,4 '-biphenyldithiol molecular junction is consistent with experimental observations in some ways.

  • 122217.
    Zou, Dapeng
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Andersson, Samir
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Zhang, Rong
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Sun, Shiguo
    Åkermark, Björn
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Selective binding of cucurbit 7 uril and beta-cyclodextrin with a redox-active molecular triad Ru(bpy)(3)-MV2+-naphthol2007In: Chemical Communications, ISSN 1359-7345, E-ISSN 1364-548X, no 45, p. 4734-4736Article in journal (Refereed)
    Abstract [en]

    A 1:1:1 inclusion complex is formed by the binding interactions among beta-CD, CB[ 7] hosts, and Ru(bpy)(3)-terminated viologen naphthalene guest in aqueous solution, in which the positions of both CB[7] and beta-CD are closer to the Ru stopper than in the respective 1:1 inclusion complexes, forming a tightened nut on bolt'' structural mode.

  • 122218.
    Zou, Dapeng
    et al.
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Andersson, Samir
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    Zhang, Rong
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Sun, Shiguo
    KTH, School of Chemical Science and Engineering (CHE), Centres, Centre of Molecular Devices, CMD.
    Åkerrnark, Björn
    Sun, Licheng
    KTH, School of Chemical Science and Engineering (CHE), Chemistry, Organic Chemistry.
    A host-induced intramolecular charge-transfer complex and light-driven radical cation formation of a molecular triad with cucurbit 8 uril2008In: Journal of Organic Chemistry, ISSN 0022-3263, E-ISSN 1520-6904, Vol. 73, no 10, p. 3775-3783Article in journal (Refereed)
    Abstract [en]

    The host-guest chemistry of systems containing a molecular triad Ru(bpy)(3)-MV2+-naphthol complex (denoted as Ru2+-MV2+-Np, 1) and cucurbit[8]uril (CB[8]) is investigated by NMR, EST-MS, UV-vis, and electrochemistry. The Ru2+-MV2+-Np guest and CB [8] host can form a stable 1:1 inclusion complex, in which the naphthalene residue is back-folded and inserted together with the viologen residue into the cavity of CB[8]. The selective binding of Ru2+-MV2+-Np guest with beta-CD and CB[8] host is also investigated. We find that CB[8] binds the Ru2+-MV2+-Np guest stronger than beta-CD. Upon light irradiation, a MV+center dot radical cation stabilized in the cavity of CB[8] accompanied by the naphthalene residue has been observed. This novel system may open a new way for design and synthesis of photoactive molecular devices.

  • 122219.
    Zou, Feng
    KTH, Superseded Departments, Materials Science and Engineering.
    Localized electrochemical impedance technique for the study of corrosion processes1998Doctoral thesis, comprehensive summary (Other scientific)
    Abstract [en]

    A localized electrochemical impedance technique has beendeveloped based on a measure of the local a.c. potentialgradient in solution by a high-resolution probe. The probeconsists of a pair of microelectrodes or a single vibratingmicroelectrode with a tip size of about 10 mm. Compared withthe experimental set-up using the bielectrode probe, the set-upusing the single vibrating-electrode probe has a highersensitivity and can be used in very low frequency range, butthe measurements by this set-up are more complex.

    Some aspects of this technique are also discussed in thethesis. The measured local a.c. potential gradient in solutionmay be related not only to the local a.c. surface currentdensity at the same location by simply using Ohm’s law asdescribed in the literature but also to the convolutionintegral of the a.c. surface current density distribution. Inorder correctly to interpret the surface current distribution,a deconvolution of the measured potential differencedistribution is necessary. The deconvolution using thebase-line stripping procedure and the Fourier Transform methodhas been investigated. The results showed that a more accuratesurface current density distribution could be obtained by thedeconvolution of the measured potential gradient distribution.In order to achieve a higher spatial resolution, the probe isnormally located as close as possible to the surface of thespecimen. However, when the probe is placed very close to thesurface, e.g. within the diffusion layer, the measurement maybe influenced by the heterogeneous distribution of ionicspecies in this range of the solution. This influence has alsobeen demonstrated and simulated. It is found that the influencecan be d.c. current-dependent when the influence ispredominately due to the variation of solution conductivity orless d.c. current-dependent when the influence is predominatelydue to the redox potential difference at different locations inthe solution. It is also noted that the influence is morepronounced in the low frequency range than in the highfrequency range.

    The technique has been used to study the pitting corrosionof Fe-Cr alloys and the degradation of organic coatings. Theresults indicate that this technique can be used not only toinvestigate the heterogeneities over the surface of a specimenwhich may be related to the localized attack, but also toobtain information about the mechanism of the localizedcorrosion by positioning the probe at the interested locationand recording the localized impedance as a function offrequency.

    Key words: corrosion, micro-electrode, electrochemicalimpedance, localized impedance technique, localized corrosion,pitting corrosion, coatings, deconvolution, diffusion.

  • 122220. Zou, H.
    et al.
    Kleiven, Svein
    KTH, School of Technology and Health (STH), Neuronic Engineering.
    Schmiedelera, J. P.
    The effect of brain mass and moment of inertia on relative brain-skull displacement during low-severity impacts2007In: International Journal of Crashworthiness, ISSN 1358-8265, E-ISSN 1754-2111, Vol. 12, no 4, p. 341-353Article in journal (Refereed)
    Abstract [en]

    Traumatic brain injury is the leading cause of death in automobile crashes. The sensitivity of human brain injury prediction to small parameter changes is a critical element of both experimental and mathematical work yet to be adequately investigated. This work proposes a new analytical human brain injury model to determine the parameters to which injury prediction is most sensitive. The trajectory sensitivity analysis explicitly indicates that injury prediction is most sensitive to brain mass moment of inertia, followed by brain mass. A number of finite element (FE) simulations were executed with various brain sizes. The maximum relative brain motions decrease with decreased brain size, and they are very close in the FE and analytical models. We conclude that brain mass moment of inertia, primarily, and brain mass, secondarily, should be varied in focused experimental and FE modeling work to ensure that conclusions are not drawn from individual data points at which injury predictions are highly sensitive to small parameter changes.

  • 122221.
    Zou, Hong
    et al.
    Department of Mechanical Engineering, The Ohio State University.
    Kleiven, Svein
    KTH, School of Technology and Health (STH), Neuronic Engineering.
    Schmiedeler, James P.
    Department of Mechanical Engineering, The Ohio State University.
    The Effect of Brain Mass and Moment of Inertia on Relative Brain-Skull Displacement in Low-Severity Impacts2006Conference paper (Refereed)
  • 122222.
    Zou, Kai
    KTH, School of Architecture and the Built Environment (ABE), Civil and Architectural Engineering, Structural Engineering and Bridges.
    Construction Methods: An International Survey of Construction Methods for Bridge Foundations2012Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
    Abstract [en]

    Bridges have become an important and common part of the infrastructure worldwide. It has been estimated that the cost of the bridge foundation construction constitutes 30% to 50% of the total bridge cost. Thus efficient and cost-saving construction methods are vital for the construction industry and for the society. For this purpose this report includes an international study of 30 bridges and their foundations, the goal of which tries to identify efficient and cost saving methods for bridge foundations.

    Ten case studies from each of North America, Europe and Asia have been included in the report including both piled (deep foundation methods) and spread footing methods.

    Large span bridges like cable-stayed bridges and suspension bridges as well as small span bridge have been included in the study. Because of the increasing popularity, special attention has been paid to the so-called integral bridge type. The case studies contain some general information about the bridge, the geological conditions at the bridge site and a brief description of the foundation methods used.

    The trend of using BIM in preliminary and detailed design of bridges is discussed in a separate section of the report. Possible advantages for adopting BIM in the design of bridge foundations such as interactive design processes are discussed.

    Bridge foundations may have a significant environmental impact including large excavations, hazardous materials, noise and etc. The important environmental impact in connection with the foundation work has been commented in another separate section called life cycle assessment.

    Finally the case studies are discussed in the conclusions section. The study, being very limited compared to the numerous bridges being built in the world, anyway gives an insight in the big challenges that are associated with bridge foundations and hopefully may give inspiration to new and efficient ways for the foundation of bridges in the future.

  • 122223. Zou, L.
    et al.
    Frampton, A.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering.
    Impacts of dead-ends on flow and transport in fractured rocks2018In: 2nd International Discrete Fracture Network Engineering Conference, DFNE 2018, American Rock Mechanics Association (ARMA) , 2018Conference paper (Refereed)
    Abstract [en]

    Detailed simulation of flow and transport through a rough-walled fracture-matrix system with fracture dead-ends is performed. The analysis demonstrates a significant impact of fracture dead-ends on fluid flow and solute transport processes in the modelled system. Two 2D representative rock fracture-matrix models with and without fracture dead-ends are constructed based on high-resolution laser-scanned measurements of a granite rock fracture surface. Simulations of flow and transport with three Péclet numbers (Pe) ranging from 0.1 to 10 are conducted using a code implementing the finite volume method (FVM) to solve the Navier-Stokes equations (NSE) for water flow in the fracture, and the advection-diffusion equation (ADE) is adopted to solve for transport in the whole fracture-matrix system, also accounting for matrix diffusion. The features of the velocity fields and evolution of concentration distributions as well as breakthrough curves of the two modelled cases are presented and analyzed, with results showing that fracture dead-ends significantly affect solute transport processes and cause important retardation of transport in the fracture. This indicates that overly conservative assessments of solute mass arrivals may be made when fracture dead-ends are ignored in discrete fracture network modelling.

  • 122224.
    Zou, Liangchao
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Numerical modeling of fluid flow and solute transport in rock fractures2016Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This study focuses on numerical modeling of fluid flow and solute transport in rough-walled rock fractures and fracture-matrix systems, with the main aim to investigate the impacts of fracture surface roughness on flow and transport processes in rock fractures. Both 2D and 3D fracture models were built from laser-scanned surface tomography of a real granite rock sample, to consider realistic features of surface tomography and potential asperity contacts. The flow was simulated by directly solving the Navier-Stokes equations (NSE) and the transport was modeled by solving the advection-dispersion equation (ADE) in the entire domain of fracture-matrix system, including matrix diffusion process. Such direct simulations provided detailed flow and concentration fields for quantitatively analysis of flow and transport behavior. The detailed analysis of surface roughness decomposition, complex flow patterns (i.e., channeling, transverse and eddy flows), effective advective flow apertures, effective transmissivity, effective dispersivity, residence time, transport resistance and specific surface area demonstrated significant impacts of realistic fracture surface roughness on fluid flow and solute transport processes in rock fractures. The results show that the surface roughness and shear displacement caused asperity contacts significantly enhance nonlinearity and complexity of flow and transport processes in rough-walled fractures and fracture-matrix systems. The surface roughness also causes invasion flows in intersected fractures which enhance solute mixing at fracture intersections. Therefore, the fracture surface roughness is an important source of uncertainty in application of such simplified models like cubic law (CL) for fluid flow and analytical solutions for solute transport in rock fractures. The research conducted advances our understanding of realistic flow and transport processes in natural fractured rocks. The results are useful for model validation/extension, uncertainty analysis/quantification and laboratory experiments design in the context of various applications related to fracture flow and transport.

  • 122225.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Modeling of advection-dominated transport in rough-walled rock fractures: a comparison of Reynolds and Navier-Stokes equationsManuscript (preprint) (Other academic)
    Abstract [en]

    Statistical analysis of flow-dependent specific surface areas of a 3D rough-walled fracture-matrix system were presented in this paper, based on numerical simulations of fluid flow and advective particle transport. The aim is to investigate the flow-dependent solute transport quantities in natural fracture-matrix systems, and identify the potential uncertainty lie in the common used flow model (i.e., Reynolds equation) by comparing with the more realistic flow model(i.e., Navier-Stokes equations). The rough-walled fracture model was built from laser-scanned surface tomography of a real rock sample, by considering realistic features of surfaces roughness and asperity contacts. Based on the flow fields simulated by solving the Reynolds and Navier-Stokes equations, the advective transport was modeled through Lagrangian particle tracking. The controlling quantities of advective transport in fracture-matrix systems (i.e., residence time, transport resistance and specific surface area) were statistically analyzed and compared. The results generally show that fracture surface roughness and associated spatially variable apertures as well as shear caused asperity contacts significantly increase the heterogeneity of flow field in rough-walled fractures, which consequently affects the flow-dependent transport process. By comparison, the simplified flow model (i.e., Reynolds equation) may cause uncertainty in quantifying of the specific surface area for the realistic rough-walled fracture-matrix systems. To identify such uncertainty, it is important to obtain the more reliable flow fields by solving the NSE. The presented results are helpful in uncertainty quantification and risk assessment of solute transport in natural fractured rocks.

  • 122226.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Roughness decomposition and effects on fluid flow in single rock fractures2014In: ISRM International Symposium - 8th Asian Rock Mechanics Symposium, ARMS 2014, International Society for Rock Mechanics , 2014, p. 457-465Conference paper (Refereed)
    Abstract [en]

    The rock fractures usually consist of surfaces with different orders or scales of roughness, which have critical effects on the fluid flow behavior inside the fractures. In this paper, a two dimensional representative single rock fracture model was built, based on a laser scanned data of rock surface of granite. The surfaces roughness of the fracture was then quantitively decomposed into several levels of surface roughness by applying the wavelet analysis. A self-developed Finite Volume Method solver was then applied to solve the Navier-Stokes equations for numerical modelling of fluid flow in the fracture models formatted with four levels of decomposed roughness, respectively, with different Reynolds numbers varying from 0.001 to 1000.0. Then, the features of velocity profiles and the effective hydraulic apertures at each level of rough fractures decomposition and Reynolds numbers were calculated and analyzed. The results show that when the Reynolds number is small (less than 10.0), the effective hydraulic aperture slightly increase nearly linearly with the decomposed roughness levels. When the Reynolds number is large, the effective hydraulic apertures decrease dramatically, and the non-linear flow behaviors represented by expansion of the eddy flow regions caused by roughness: The larger extent of high-frequency roughness, the more obvious and complicate eddy flow regions yielded.

  • 122227.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Håkansson, U.
    KTH.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Impacts of elastic jacking on rock grouting2018In: ISRM International Symposium - 10th Asian Rock Mechanics Symposium, ARMS 2018, International Society for Rock Mechanics , 2018Conference paper (Refereed)
    Abstract [en]

    The injection pressure is an important design and operational parameter in rock grouting since it controls the grout penetration length and may cause harmful mechanical deformation of the rock mass, such as opening/dilation of the fractures, referred to as jacking. At present, modeling of rock grouting mainly relies on analytical models where the impact of jacking on the grout penetration in rock fractures is not considered. In this study, we present a hydro-mechanical coupled model for rock grouting in a single one-dimensional rock fracture, with consideration of jacking and two-phase flow, i.e. cement grout and groundwater. It assumes that the cement grouts are Bingham fluids and that the rock matrix is an elastic material. The fracture is simplified as a pair of smooth parallel plates. A finite element method (FEM) code is developed to iteratively solve the two-phase flow in the fracture and the elastic deformation of the rock matrix. Two cases with and without consideration of jacking are simulated and compared. The results generally show that jacking of fractures significantly affects the grout penetration in the fracture, which should be properly considered in modeling of rock grouting. This numerical model is able to describe more realistic physical processes in rock grouting, which can be used to estimate the optimal injection pressure in practice. 

  • 122228.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Håkansson, Ulf
    KTH, School of Architecture and the Built Environment (ABE), Civil and Architectural Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Cement grout propagation in two-dimensional fracture networks: Impact of structure and hydraulic variability2019In: International Journal of Rock Mechanics And Mining Sciences, ISSN 1365-1609, E-ISSN 1873-4545, Vol. 115, p. 1-10Article in journal (Refereed)
    Abstract [en]

    Analysis of cement grout propagation in water-saturated two-dimensional discrete fracture networks is presented in this study. A two-phase flow model for Bingham fluids flow in a single saturated fracture is extended to simulate cement grouts propagation in saturated networks. Using this extended model, the impacts of network structure and hydraulic variability, i.e., network geometry and aperture distribution, on the propagation process are investigated through numerical simulations. Cement grout propagation in 50 realizations of a two-dimensional discrete fracture network (2D DFN) are simulated with different cases of aperture variability, i.e. constant aperture, uncorrelated and length-correlated heterogeneous apertures following a truncated lognormal distribution. The results indicate that network structure and hydraulic variability significantly affect the grout propagation in 2D DFN systems. The randomized network structure and uncorrelated heterogeneous apertures significantly delay the propagation rate and largely increase the variability range of the propagation volume fraction. In contrast, in the case with length-correlated heterogeneous apertures, the propagation rate increases, while the variability range and rate of change of the propagation volume fraction decreases. The extended two-phase flow model for fracture networks and the simulation results presented in this work are useful for basic understanding of the processes relevant for design, monitoring and execution of rock grouting.

  • 122229.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Håkansson, Ulf
    KTH, School of Architecture and the Built Environment (ABE), Civil and Architectural Engineering, Soil and Rock Mechanics.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Modeling of rock grouting in saturated variable aperture fractures2018In: Proceedings of Bergdagarna 2018., 2018, p. 79-87, article id 10Conference paper (Refereed)
    Abstract [en]

    Modeling and analysis of cement grouts flow in rock fractures is important in the design, execution and monitoring of grouting in fractured rocks. At present, modeling of rock grouting mainly relies on analytical models, e.g., the real time grouting control (RTGC) method. In the RTGC method, it is assumed that the rock fractures are consisting of smooth parallel plates or disks and water flow is neglected. However, in reality, the natural rock fractures are commonly consisting of complex rough-walled surfaces and are filled with groundwater; therefore, grouting is actually a multiphase (non-Newtonian grouts and groundwater) flow process in rough-walled rock fractures with variable apertures. In this study, we present an efficient one-dimensional (1D) numerical model for modeling of rock grouting in a single rock fracture with consideration of multiphase flow and variable apertures. It is assumed that the cement grouts are Bingham fluids and that the analytical solution for flowrate with a given pressure gradient in a pair of smooth parallel plates is locally applicable. A time-dependent advection equation is used to describe the interface (between the grout and groundwater) propagation. A finite element method (FEM) code is developed to iteratively solve the mass balance and the interface advection equations. The numerical simulations are compared with the RTGC method. It generally shows that water flow significantly affect grouts penetration in the fracture, especially for the grouts with relatively lower viscosity. The variable aperture significantly postpones the penetration process compared with that of constant aperture. This numerical model is able to describe more realistic physical processes and geometry conditions in rock grouting, which can be readily used in practice to reduce the potential uncertainties in application of simplified analytical models.

  • 122230.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Håkansson, Ulf
    KTH, School of Architecture and the Built Environment (ABE), Civil and Architectural Engineering, Soil and Rock Mechanics. Skanska AB .
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Non-Newtonian grout flow in single rough-walled rock fractures2019Conference paper (Refereed)
    Abstract [en]

    Modeling of cement grout flow in rock fractures plays an important role in the design of rock grouting. Cement grouts used in rock grouting practice are typical non-Newtonian fluids containing yield stress, and are often assumed as Bingham fluids. Natural rock fractures typically consist of rough surfaces. Therefore, in reality, rock grouting process actually involves non-Newtonian fluid flow in rough-walled fractures, which is rarely studied in the literature. In this work, we focus on the impact of surface roughness and present direct numerical simulations of non-Newtonian grouts flow in single rough-walled fractures, using a regularized method to approximate the yield-stress. The rough-walled rock fracture models are created from a laser-scanned surface of a granite rock sample, to represent realistic features of natural rock fractures. The numerical results generally show nonlinear behaviors of non-Newtonian fluid flow in rough-walled fractures. The surface roughness significantly reduces the effective transmissivity when Reynolds number is relatively large. The obtained result can be used for upscaling analysis in practice, in order to reduce the potential uncertainties caused by the surface roughness of the rock fractures.

    The full text will be freely available from 2020-01-01 23:22
  • 122231.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Håkansson, Ulf
    KTH, School of Architecture and the Built Environment (ABE), Civil and Architectural Engineering, Soil and Rock Mechanics.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Two-phase cement grout propagation in homogeneous water-saturated rock fractures2018In: International Journal of Rock Mechanics And Mining Sciences, ISSN 1365-1609, E-ISSN 1873-4545, Vol. 106, p. 243-249Article in journal (Refereed)
    Abstract [en]

    Modeling of cement grout flow in rock fractures is important for the design, monitoring and execution of rock grouting that is widely used in a variety of rock engineering applications. This study presents a mathematical model based on the Reynolds flow equation for cement grout flow in a homogeneous water-saturated rock fracture. The model is based on two-phase flow, i.e. grout as a Bingham fluid and groundwater as a Newtonian fluid, and is used for investigating the importance of the water phase in rock grouting. The modeling results for the two-phase flow generally show the importance of the water phase that can significantly affect the pressure distribution and grout penetration in the fracture, especially under the condition of grout hardening. Such effects depend on the viscosity ratio between the grout and groundwater, which becomes increasingly important for cases with smaller values of the viscosity ratio. The grout density also affects the grout penetration length. Applying an analytical solution based on single-phase flow, i.e. neglecting the impact of groundwater flow, for modeling grout injection, will generally overestimate the penetration length.

  • 122232.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Smoothed particle hydrodynamics simulation of fluid flow in rock fractures2013In: Rock Characterisation, Modelling and Engineering Design Methods: Proceedings of the 3rd ISRM SINOROCK 2013 Symposium, 2013, p. 437-443Conference paper (Refereed)
    Abstract [en]

    The process of fluid flow in rock fractures involves complicated dynamical behavior of fluids,and its modeling is a challenge to numerical methods. In this paper, the Smoothed Particle Hydrodynamics(SPH), a particle method based on Lagrangian formulation, is employed to simulate the fluid flow in rockfractures by solving the Navier-Stokes equations directly. Firstly, the SPH method and the boundary treatmentmethod used in this simulation were introduced and the computer code of SPH was developed and validated bya series of numerical benchmark tests with analytical solutions. Then simulations were carried out to investigatethe fluid flow both in single fractures and intersected fractures, with and without considering effects of surfaceroughness. The results of the simulations are discussed and compared with the analytical solution by using theCubic law derived from the Reynolds equation. The results show that in both of rough single fractures andfracture intersections, although the relationship between mean velocity and the Reynolds number is still linear,the solutions by using Cubic law overestimated the mean fluid velocity with increasing the Reynolds number,indicating possible underestimate of travel time of mass transport in the fracture network models.

  • 122233.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Assumptions of the analytical solution for solute transport in a fracture-matrix system2016In: International Journal of Rock Mechanics And Mining Sciences, ISSN 1365-1609, E-ISSN 1873-4545, Vol. 83, p. 211-217Article in journal (Refereed)
  • 122234.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Effect of sorption on solute transport in a single rough rock fracture2017In: 13th ISRM International Congress of Rock Mechanics, International Society for Rock Mechanics , 2017Conference paper (Refereed)
    Abstract [en]

    Sorption process plays a significant role for solute retardation in rock fractures. In this paper, for the aim to investigate the effect of sorption on solute transport in a single rough fracture, a 2D model of representative single rock fracture was built and its roughness was statistically characterized based on the measured data of rock surface topography by laser scanning. A Finite Volume Method (FVM) code was developed to solve the Navier-Stokes (NS) equations and transport equation for numerical modelling the process of fluid flow and solute transport in the rock fracture model. Two groups of simulations were conducted: with and without the consideration of the sorption process with different average flow velocities. The results show that the surface roughness increased the complexities of flow fields, and the non-linear sorption process plays a significant role in the retardation of solute transport through rock fractures. The sorption process caused an obvious lagging time in both the solute concentration fields (plumes) and corresponding breakthrough curves. This lagging time increases with the distance from the inlet boundary, and relatively decreases with the increase of mean velocities.

  • 122235.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Effects of multi-level surface roughness on solute transport in single rock fractures2016In: The proceeding of International Symposium on Reducing Risks in Site Investigation, Modeling and Construction for Rock Engineering, 2016Conference paper (Refereed)
    Abstract [en]

    Natural rock fractures are consisted of complicate rough surfaces with multi-level surface roughness which causes significant uncertainties in fluid flow and solute transport be-haviors through fractured rocks. In this study, for the aim of investigation the effects of multi-level surface roughness on fluid flow and solute transport in rock fractures, a single rough-walled fracture model was built from a scanned granite rock surface, which was then gradually decomposed and characterized by wavelet analysis and statistics. A verified finite volume method (FVM) code was used to simulate fluid flow and solute transport in the rough fracture models by solving the Navier-Stokes equations (NSE) and advection-dispersion equation (ADE). The simulation results of nonlinear flow and solute breakthrough curves (BTCs) showed that the multi-level surface roughness strongly correlated with the Eddy flows and the solute non-Fickian transport behaviors, represented by the changes of effective advective flow apertures and an empirical function of the BTCs. The results would improve our understanding of solute transport in fractured rocks and may help to reduce the uncertainties and risks in related engi-neering practices.

  • 122236.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Effects of Sorption on Solute Transport in a Single Rough Rock Fracture2015Conference paper (Refereed)
    Abstract [en]

    The sorption process plays a significant role in the retardation of solute transport through the fractures. In this paper, based on the measured data of rock surfaces by laser scanning, a 2D geometry model of a representative single rock fracture was built and its roughness was statistically characterized, and a Finite Volume Method (FVM) code was developed and applied to solve the NS equation and transport equation for numerical modelling the process of fluid flow and solute transport. Two groups of simulation were then calculated: with and without the consideration of the sorption process, with different average flow velocities. The effects of sorption on the solute transport process were then analyzed, discussed and followed by concluding remarks on the sorption impact on the understanding of mass transport process in fractured rock masses.

  • 122237.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Invasion flow enhanced solute mixing at rough-walled rock fracture intersectionsManuscript (preprint) (Other academic)
    Abstract [en]

    The processes of fluid flow and solute transport through rock fractures are of primary importance in environmental engineering and geosciences. This study presented numerical modeling results of fluid flow and solute transport in a 3D rock fracture-matrix system with an orthogonal intersection of two rough-walled rock fractures. The rough-walled fracture geometry models were built from laser-scanned data of a real rock surface, for a realistic representation of natural rock fracture surface roughness. The fluid flow in the two intersected fractures and solute transport in the fracture-matrix system were simulated by solving the Navier-Stokes equations (NSE) and transport equation in the entire system. The dependence of mixing on Péclet number (Pe), flow directionality and interaction with matrix diffusion were analyzed. The results showed important invasion flow patterns that significantly enhanced the solute mixing process, which cannot be described by traditional complete mixing and streamline routing models. It also cannot be simulated by simplified 2D geometry models ignoring the surface roughness as widely used in previous published studies. The finding of invasion flow and associated impacts on mixing in this study is particularly important in prediction of solute transport in natural fractured rocks, especially when discrete fracture network (DFN) approach is applied.

  • 122238.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Modeling of flow and mixing in 3D rough-walled rock fracture intersections2017In: Advances in Water Resources, ISSN 0309-1708, E-ISSN 1872-9657, Vol. 107, p. 1-9Article in journal (Refereed)
    Abstract [en]

    The processes of fluid flow and solute transport through rock fractures are of primary importance in environmental engineering and geosciences. This study presented numerical modeling results of fluid flow and solute transport in a 3D rock fracture-matrix system with an orthogonal intersection of two rough-walled rock fractures. The rough-walled fracture geometry models were built from laser-scanned data of a real rock surface, for a realistic representation of natural rock fracture surface roughness. The fluid flow in the two intersected fractures and solute transport in the fracture-matrix system were simulated by solving the Navier–Stokes equations (NSE) and transport equation in the entire system. The dependence of mixing on Péclet number (Pe) and flow directionality features were analyzed. The results directly visualized important channeling flow patterns that significantly enhanced the solute mixing process at the rough-walled fracture intersection. The illustrated channeling flow and associated impacts on mixing are particularly important in the prediction of solute transport in natural fractured rocks, especially when discrete fracture network (DFN) approach is applied.

  • 122239.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Modeling of Solute Transport in a 3D Rough-Walled Fracture-Matrix System2017In: Transport in Porous Media, ISSN 0169-3913, E-ISSN 1573-1634, Vol. 116, no 3, p. 1005-1029Article in journal (Refereed)
    Abstract [en]

    Fluid flow and solute transport in a 3D rough-walled fracture-matrix system were simulated by directly solving the Navier-Stokes equations for fracture flow and solving the transport equation for the whole domain of fracture and matrix with considering matrix diffusion. The rough-walled fracture-matrix model was built from laser-scanned surface tomography of a real rock sample, by considering realistic features of surfaces roughness and asperity contacts. The numerical modeling results were compared with both analytical solutions based on simplified fracture surface geometry and numerical results by particle tracking based on the Reynolds equation. The aim is to investigate impacts of surface roughness on solute transport in natural fracture-matrix systems and to quantify the uncertainties in application of simplified models. The results show that fracture surface roughness significantly increases heterogeneity of velocity field in the rough-walled fractures, which consequently cause complex transport behavior, especially the dispersive distributions of solute concentration in the fracture and complex concentration profiles in the matrix. Such complex transport behaviors caused by surface roughness are important sources of uncertainty that needs to be considered for modeling of solute transport processes in fractured rocks. The presented direct numerical simulations of fluid flow and solute transport serve as efficient numerical experiments that provide reliable results for the analysis of effective transmissivity as well as effective dispersion coefficient in rough-walled fracture-matrix systems. Such analysis is helpful in model verifications, uncertainty quantifications and design of laboratorial experiments.

  • 122240.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Modeling of solute transport in a 3D rough-walled fracture-matrix systemManuscript (preprint) (Other academic)
    Abstract [en]

    Fluid flow and solute transport in a 3D rough-walled fracture-matrix system was simulated by directly solving the Navier-Stokes equations for fracture flow and solving the transport equation for the whole domain of fracture and matrix with considering matrix diffusion. The rough-walled fracture-matrix model was built from laser-scanned surface tomography of a real rock sample, by considering realistic features of surfaces roughness and asperity contacts. The numerical modeling results were compared with both analytical solutions based on simplified fracture surface geometry and numerical results by particle tracking based on the Reynolds equation. The aim is to investigate impacts of surface roughness on solute transport in natural fracture-matrix systems, and to quantify the uncertainties in application of simplified models. The results show that fracture surface roughness significantly increases heterogeneity of velocity field in the rough-walled fractures, which consequently cause complex transport behavior, especially the dispersive distributions of solute concentration in the fracture and complex concentration profiles in the matrix. Such complex transport behavior caused by surface roughness are important sources of uncertainty that needs to be considered for modeling of solute transport processes in fractured rocks. The presented direct numerical simulations of fluid flow and solute transport serve as efficient numerical experiments that provide reliable results for the analysis of effective transmissivity as well as effective dispersion coefficient in rough-walled fracture-matrix systems. Such analyses are helpful in model verifications, uncertainty quantifications and design of laboratorial experiments.

  • 122241.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Roughness decomposition and nonlinear fluid flow in a single rock fracture2015In: International Journal of Rock Mechanics And Mining Sciences, ISSN 1365-1609, E-ISSN 1873-4545, Vol. 75, p. 102-118Article in journal (Refereed)
    Abstract [en]

    The objective of this paper is to investigate the effects of wall surface roughness on fluid flow through rock fractures. A wavelet analysis technique was developed to define a mathematical criterion for decomposing the original wall surface roughness profiles of a fracture into a high-frequency (secondary roughness) profile and a low-frequency (primary roughness) profile, in order to examine their impacts on fluid flow, by solving the Navier-Stokes equations (NSE) without linearization, using a self-developed 2D finite volume method (FVM) code. The results indicate that the high-frequency secondary roughness is the main cause for dynamic evolution of Eddy flow regions in the fracture flow field, besides the Reynolds number (Re). In the original fracture model with the high-frequency secondary roughness, our results show that fluid flow fields are not only generally non-linear, but also with non-stop generation and motions of eddies in the boundary layer regions of rough fractures when the Re = 1000 in this study, which will affect the solute transport processes in fractured rock masses. The complete NSE were solved without removing acceleration and inertial terms, so that the impacts of surface roughness on the nonlinear and dynamic flow behavior of rock fractures were calculated and visualized more accurately, which is important for modeling mass and energy transport processes in fractures and fractured rock masses.

  • 122242.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering. KTH.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Shear enhanced nonlinear flow in rough-walled rock fracturesManuscript (preprint) (Other academic)
    Abstract [en]

    Nonlinear flow in 3D rough-walled rock fracture models are simulated by solving the Navier-Stokes equations in this paper. The emphasis is on the impacts of shear caused aperture changes (variable apertures and asperity contacts) and flow conditions (inertial term) upon nonlinear flow behaviors in 3D rough-walled rock fractures. In order to compare shear effects, two 3D fracture models, with and without shear process, were established with the identical initial rough-walled surfaces tomography of a realistic rock sample. Five groups of simulations with different inflow boundary conditions of flowrates/Reynolds numbers (Re) were conducted to demonstrate shear enhanced nonlinearity of flow fields and limitations of local cubic law (LCL) approach. The flow results clearly show channeling flow along the preferential fluid paths, transverse flow around the contact spots and eddy flows behind contact spots with increasing Re numbers, which cannot be observed in 2D models. The effective transmissivity of the 3D fracture model was calculated from the modeling results of velocity and pressure fields. The results showed that the effective transmissivity is a function of local apertures with important uncertainties even when Re is small (i.e. Re = 0.4 in this study), thus the validity of the transmissivity evaluation using LCL approach for nonlinear flow in 3D rough-walled rock fractures is questionable. The mechanical effects, i.e. stress and shear caused aperture space changes and asperity contacts should be considered for modeling flow and mass/energy transport processes in rough-walled fractures in 3D.

  • 122243.
    Zou, Liangchao
    et al.
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Jing, Lanru
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Land and Water Resources Engineering.
    Cvetkovic, Vladimir
    KTH, School of Architecture and the Built Environment (ABE), Sustainable development, Environmental science and Engineering, Resources, Energy and Infrastructure.
    Shear-enhanced nonlinear flow in rough-walled rock fractures2017In: International Journal of Rock Mechanics And Mining Sciences, ISSN 1365-1609, E-ISSN 1873-4545, Vol. 97, p. 33-45Article in journal (Refereed)
    Abstract [en]

    Nonlinear flow in 3D rough-walled rock fractures is simulated by solving the Navier-Stokes equations. The emphasis is on the impact of shear-caused aperture changes (variable apertures and asperity contacts) and flow conditions (inertial term) upon nonlinear flow behavior. In order to compare shear effects, two 3D fracture models, with and without shear, were established with identical initial rough-walled surfaces topographies of a realistic rock sample. Five groups of simulations with different inflow boundary conditions of flowrates/Reynolds numbers (Re) were conducted to demonstrate shear-enhanced nonlinearity of flow fields and limitations of local cubic law (LCL) approach. The flow results clearly show channeling flow along the preferential paths, transverse flow around the contact spots, and eddy flows behind contact spots with increasing Re, which cannot be observed in 2D models. The effective transmissivity of the 3D fracture model was calculated from the modeling results of velocity and pressure fields. The results showed that the effective transmissivity is a function of local apertures with important uncertainties even when Re is small (i.e. Re = 0.4 in this study), thus the validity of the transmissivity evaluation using LCL approach for nonlinear flow in 3D rough-walled rock fractures is questionable.

  • 122244. Zou, Qi
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Xu, Qunjie
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhao, Wandong
    Qu, Yi
    A near-infrared "on-off" fluorescent and colourimetric cyanide chemodosimeter based on phenothiazine with applications in living cell imaging2014In: RSC Advances, ISSN 2046-2069, E-ISSN 2046-2069, Vol. 4, no 104, p. 59809-59816Article in journal (Refereed)
    Abstract [en]

    A great deal of effort has been devoted to developing easy-to-use near-infrared probes for detecting analytes due to their advantages in the field of biosensing. Herein, a near-infrared "on-off" fluorescent chemodosimeter PTZ based on dicyano-vinyl-functionalised phenothiazine was designed and synthesised. The PTZ compound was shown to efficiently recognise cyanide ions in aqueous media by virtue of the special nucleophilicity of cyanide ions, which affects the intramolecular charge transfer efficiency in the molecule. Furthermore, it was found that it exhibited a rapid colourimetric and quenchable near-infrared (NIR) fluorescent response to cyanide ions with a detection limit as low as 67 nM, and that other anions showed almost no interference even at high concentrations. Optical spectroscopic measurements, H-1 NMR and mass spectrometry titrations, and theoretical simulations were carried out to elucidate the sensing mechanism of compound PTZ. Moreover, potential applications of this compound for biosensing have been exemplified by the successful fluorescent microscopic imaging for the detection of cyanide ions in HeLa cells.

  • 122245. Zou, Qi
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Zhou, Ji
    Bai, Kangkang
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Synthesis and photochromism of a spirooxazine derivative featuring a carbazole moiety: Fast thermal bleaching and excellent fatigue resistance2014In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 107, p. 174-181Article in journal (Refereed)
    Abstract [en]

    A novel photochromic spirooxazine derivative bearing a carbazole moiety (SOC) was synthesized and studied in solution under flash photolysis conditions. It is found to exhibit excellent characteristics like high photochromic response, large steady-state optical density, fast thermal bleaching rate and good fatigue-resistance. The effect of different solvents on the photochromic properties of the compound was evaluated, revealing that the photochromic properties can be modulated by different solvents based on the corresponding polarity. The mechanism and kinetics of the thermal fading process of compound SOC were additionally investigated by theoretical simulations, where the isomerization pathway from the trans-trans-cis conformation was found to be several times faster than that from the cis-trans-cis conformation. This type of fast-bleaching and fatigue-resistent photochromic compounds is expected to pave an exciting avenue in future development of high-performance photochromic materials.

  • 122246. Zou, Qi
    et al.
    Li, Xin
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Biotechnology (BIO), Theoretical Chemistry and Biology.
    Configurable photochromism of an unsymmetrical dithienylethene derivative by Cu2+ ions or water2014In: Dyes and pigments, ISSN 0143-7208, E-ISSN 1873-3743, Vol. 111, p. 1-7Article in journal (Refereed)
    Abstract [en]

    We describe a gated photochromic behavior of an unsymmetrical dithienylethene derivative, which is intrinsically inert to photoisomerization in organic solvents and which is activated by addition of Cu2+ ions or water. The mechanism behind the gated photochromic property is interpreted by theoretical simulations, suggesting that the energy levels of frontier molecular orbitals are altered by the interaction of the Schiff base moiety with Cu2+ ions or water molecules. Potential applications of such gated photochromic materials have been exemplified not only by the reversible interchange between the photoactive and photoinactive states triggered by Cu2+ ions and EDTA, but also by the construction of a keypad with sequence-dependent input signals at the molecular level.

  • 122247.
    Zou, Rongfeng
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Computational Studies of Protein-ligand Systems Using Enhanced Sampling Methods2019Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    This thesis focuses on studies of protein-ligand systems using enhanced sampling methods. In chapter I, I give a brief introduction to the time-scale problem and some enhanced sampling methods. In chapter II, the basics of MD simulation are reviewed. In chapter III, the theoretical backgrounds of umbrella sampling, bias-exchange metadynamics and infrequent metadynamics are presented. In chapter IV, the 5 papers included in this thesis are summarized. In paper 1, we studied the relationship between the antibacterial activities of antimicrobial peptides and their aggregation propensities. We found that an increasing aggregation propensity increases the free energy cost of peptide embedding into the bacterial membrane and decreases antibacterial activity. In paper 2, we employed the umbrella sampling approach to obtain the free energy landscape of Pittsburgh compound-B penetrating into the core binding sites of amyloid βfibrils. Our study suggested that, for the design of probes binding to fibril like proteins, other than the binding affinity, the dynamics of probes in the fibrils should also be considered. In paper 3, we studied the coupled folding and binding process of the intrinsically disordered protein p53 to MDM2 with bias-exchange metadynamics and infrequent metadynamics. We reconstructed the free energy landscape and built a kinetic network for this process. In paper 4, we studied the binding modes of ASEM with a chimera structure of α7 nicotinic acetylcholine receptor with well-tempered metadynamics. We found that an important residue, Trp53, can significantly affect the stabilities of the binding modes. In paper 5, we proposed an efficient method to estimate the transition times of rare events in biomolecular systems. In chapter V, I present a conclusion of this thesis and propose an outlook related to the selection of collective variables for enhanced sampling methods.

  • 122248.
    Zou, Rongfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Guanglin, Kuang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology. Henan Univ, Coll Chem & Chem Engn, Kaifeng 475004, Henan, Peoples R China..
    Nordberg, Agneta
    Karolinska Univ Hosp, Karolinska Inst, Dept Neurobiol Care Sci & Soc, Ctr Alzheimer Res,Clin Geriatr Neo & Theme Aging, S-14183 Huddinge, Sweden..
    Långström, Bengt
    Uppsala Univ, Phys Organ Chem, Dept Chem, BMC, S-75123 Uppsala, Sweden..
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Free Energy Profile for Penetration of Pittsburgh Compound-B into the Amyloid beta Fibril2019In: ACS Chemical Neuroscience, ISSN 1948-7193, E-ISSN 1948-7193, Vol. 10, no 3, p. 1783-1790Article in journal (Refereed)
    Abstract [en]

    The amyloid beta (A beta) fibril is a hallmark of Alzheimer's disease (AD) and has therefore served as an important target for early diagnosis of AD. The Pittsburgh Compound-B (PiB) is one of the most famous positron emission tomography (PET) tracers commonly used for in vivo detection of A beta fibrils. Many theoretical studies have predicted the existence of various core binding sites with different microenvironments for probes binding to the A beta fibril. However, little attention has been devoted to how the probes actually penetrate into the different core binding sites. In this study, an integrated molecular modeling scheme is used to study the penetration of PiB into the core binding sites of the A beta(1-42) fibril structure recently obtained by cryogenic electron microscopy. We find that there are two core binding sites for PiB with dramatic differences in cavity size and microenvironment properties, and furthermore that the penetration of PiB into site-1 is energetically prohibitive, whereas the penetration into site 2 is much more favorable. Therefore, the binding capacity at site-2 may be larger than that at site-1 despite its lower binding affinity. Our results thus suggest that site-2 may be a major binding site for PiB binding to A beta fibril and emphasize the importance to adopt a full dynamical picture when studying tracer fibril binding problems in general, something that in turn can be used to guide the development of tracers with higher affinity and selectivity for the A beta fibril.

  • 122249.
    Zou, Rongfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Wang, Yong
    Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    An Efficient Strategy for the Estimation of Rare Event Transition Times in Biomolecular SystemsManuscript (preprint) (Other academic)
    Abstract [en]

    Studies of kinetics in biological systems are important for understanding functions of biomolecules and can provide valuable information for drug discovery. However, how to obtain the kinetics closely related to a rare event occurring in a biomolecular system from conventional unbiased molecular dynamics (MD) simulations remains a big challenge. Recently, an enhanced sampling method, namely infrequent metadynamics (InMetaD), has been developed and has the capability to recover the unbiased transition time from metadynamic runs. However, in this method a bias potential is deposited to the system at a low frequency, which often makes most of the computational time spend in waiting for the simulated system escaping from the initial state. Here we propose a strategy to achieve the same goal as InMetaD with increased efficiency. In this strategy, we first accelerate the occurring of a rare event using metadynamics simulations with a high bias deposition frequency, and subsequently restart the simulations at a time point before the rare event occurs, but with a low bias deposition frequency. Through combining these simulation data, the unbiased transition time can be recovered in the same way as in InMetaD. We applied this strategy to the studies of three systems including the conformational change of a small peptide, unfolding of a protein, and unbinding of an intrinsically disordered protein from its target. We show that our strategy can improve the efficiency in estimating the unbiased transition times in a very convenient way.

  • 122250.
    Zou, Rongfeng
    et al.
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Zhou, Yang
    KTH, School of Engineering Sciences (SCI), Mechanics, Structural Mechanics.
    Wang, Yong
    Structural Biology and NMR Laboratory, Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen.
    Guanglin, Kuang
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Ågren, Hans
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH).
    Wu, Junchen
    Key Laboratory for Advanced Materials & Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology.
    Tu, Yaoquan
    KTH, School of Engineering Sciences in Chemistry, Biotechnology and Health (CBH), Theoretical Chemistry and Biology.
    Free Energy Profile and Kinetics for Coupled Folding and Binding of the Intrinsically Disordered Protein p53 with MDM2Manuscript (preprint) (Other academic)
    Abstract [en]

    Intrinsically disordered proteins (IDPs) exert their functions by binding to partner proteins via a complex process that includes coupled folding and binding. Motivated by that inhibiting the binding of the IDP p53 to its partner MDM2 has become a promising strategy for drug design and that understanding of this process poses a most significant challenging task, we present an atomistic level simulation of the coupled folding and binding process linking the IDP p53 to MDM2. Using bias-exchange metadynamics (BE-MetaD) and infrequent metadynamics (InMetaD) we estimate the binding free energy, the unbinding rate and the binding rate. By analyzing the stable intermediates, we uncover the role of nonnative interactions played in the p53-MDM2 binding/unbinding process. We use a three-state model to describe the whole binding/unbinding process and to obtain the corresponding rate constants. Our work shows that the binding of p53 favors an induced fit mechanism which proceeds in a stepwise fashion. In general, InMetaD gave consistent results with BE-MetaD in terms of binding mechanism and intermediates, proving the robustness of our studies of the p53-MDM2 system using metadynamics. The results contribute to the in-depth understanding for the coupled folding and binding process that is needed for the design of MDM2 inhibitors.

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