Distance matters: the impact of gene proximity in bacterial gene regulation

Following recent discoveries of colocalization of downstream-regulating genes in living cells, the impact of the spatial distance between such genes on the kinetics of gene product formation is increasingly recognized. We here show from analytical and numerical analysis that the distance between a transcription factor (TF) gene and its target gene drastically affects the speed and reliability of transcriptional regulation in bacterial cells. For an explicit model system we develop a general theory for the interactions between a TF and a transcription unit. The observed variations in regulation efficiency are linked to the magnitude of the variation of the TF concentration peaks as a function of the binding site distance from the signal source. Our results support the role of rapid binding site search for gene colocalization and emphasize the role of local concentration differences.Comment: 5 pages, 2 figures; Supplementary material contained in the source file

Polymer dynamics in time-dependent periodic potentials

Dynamics of a discrete polymer in time-dependent external potentials is studied with the master equation approach. We consider both stochastic and deterministic switching mechanisms for the potential states and give the essential equations for computing the stationary state properties of molecules with internal structure in time-dependent periodic potentials on a lattice. As an example, we consider standard and modified Rubinstein-Duke polymers and calculate their mean drift and effective diffusion coefficient in the two-state non-symmetric flashing potential and symmetric traveling potential. Rich non-linear behavior of these observables is found. By varying the polymer length, we find current inversions caused by the rebound effect that is only present for molecules with internal structure. These results depend strongly on the polymer type. We also notice increased transport coherence for longer polymers.Comment: 22 pages, 7 figure

Ensemble Forecasting of Major Solar Flares -- First Results

We present the results from the first ensemble prediction model for major solar flares (M and X classes). The primary aim of this investigation is to explore the construction of an ensemble for an initial prototyping of this new concept. Using the probabilistic forecasts from three models hosted at the Community Coordinated Modeling Center (NASA-GSFC) and the NOAA forecasts, we developed an ensemble forecast by linearly combining the flaring probabilities from all four methods. Performance-based combination weights were calculated using a Monte-Carlo-type algorithm that applies a decision threshold $P_{th}$ to the combined probabilities and maximizing the Heidke Skill Score (HSS). Using the data for 13 recent solar active regions between years 2012 - 2014, we found that linear combination methods can improve the overall probabilistic prediction and improve the categorical prediction for certain values of decision thresholds. Combination weights vary with the applied threshold and none of the tested individual forecasting models seem to provide more accurate predictions than the others for all values of $P_{th}$. According to the maximum values of HSS, a performance-based weights calculated by averaging over the sample, performed similarly to a equally weighted model. The values $P_{th}$ for which the ensemble forecast performs the best are 25 \% for M-class flares and 15 \% for X-class flares. When the human-adjusted probabilities from NOAA are excluded from the ensemble, the ensemble performance in terms of the Heidke score, is reduced.Comment: Accepted for publication in Space Weathe

Nanoparticles of Gold and Copper : Sintering and Supramolecular Assembly Investigations

Nanoparticles of gold, copper and copper sulfide with different kinds of protective ligands were successfully synthesized and characterized. Of special interest were particles protected with calixarenes, and their complexation with guest molecules. The copper sulfide nanocrystals were protected with benzyl thiol moieties that were generated by reducing RAFT chain transfer agent in the particle synthesis. The nanocrystals were characterized in detail and their sintering on paper was studied. The as-prepared crystals were in Cu2S (chalcocite) form, but thermal sintering resulted in the consolidation of the crystallites as well as the transformation of the material into a semiconductive Cu1.8S (digenite) film. The metallic copper nanoparticles were obtained by reducing copper salts in the presence of polyethylene imine (PEI) or analogous small organic compounds (tetraethylene pentamine, TEPA). In the case of the polymer, the strong complexation of the copper ions into the polymer matrix retarded the reduction reaction enabling the preparation of crystallites with less than 10 nm diameter. The particles were coated with a surface oxide layer that catalyzed the thermal decomposition of the PEI protecting layer, resulting in low sintering temperatures for the nanoparticles. The sacrificial decomposition of PEI resulted in reduction of the oxide layer back into metallic copper. The particles were sintered on paper and the layers were found to be semiconductive. Calix[4]arene protected gold nanoparticles were prepared and the interactions of pyridinium with the calixarene cavity was examined in great detail. It was found that the calixarenes bound to the gold surface are able to complex pyridinium cations, and that the complexation induced the aggregation of the nanoparticles. Further, the complexing ability of the calixarene could be tuned by preparing mixed monolayers of calixarenes and alkanethiols: key factors were the amount of calixarene in the mixed monolayer, the calixarene type and the length of the calixarene spacer, as well as the length of the alkanethiol chain. Finally, alkanethiol protected gold nanoparticles were prepared, inkjetted and sintered to form an electrode on paper. The results indicated the electrode was of comparable electronic quality to gold electrodes printed onto glass substrates. In this way, gold nanoparticles can be used in inexpensive roll-to-roll printed paper-based electronic platforms.Tässä tutkimuksessa syntetisoitiin eri suojausaineilla pinnoitettuja kulta-, kuparisulfidi- ja kuparinanopartikkeleita. Partikkelien rakenne ja koostumus karakterisoitiin eletronimikroskopialla (TEM), termogravimetrialla (TGA) ja ydinmagneettisella resonanssispektroskopialla (NMR). Kultapartikkeliin kiinnitettyjen kaliksareenimolekyylien kompleksaatiota orgaanisten pyridiniumkationien kanssa seurattiin NMR:llä, valonsironnalla (LS) ja UV-Vis spektroskopialla. Tioli- tai aminoyhdisteillä suojattujen kulta-, kuparisulfidi- ja kuparipartikkelien sintrausominaisuuksia tutkittiin röntgensirontamenetelmin. Kuparisuolan pelkistäminen RAFT-ketjunsiirtoreagenssin läsnäollessa havaittiin muodostavan bentsyylitiolisuojattuja kuparisulfidipartikkeleita. Partikkelit olivat kuparisulfidia Cu2S-muodossa, mutta terminen sintraus paperisubstraatille johti suojausaineen termisen hajoamisen kautta kiteiden yhdistymiseen puolijohtavaksi Cu1.8S-kerrokseksi. Metallisia kuparinanopartikkeleita syntetisoitiin käyttämällä amiinipohjaisia yhdisteitä (polyetyleeniimiini ja tetraetyleenipentamiini) suojausaineina. Polymeerisen suojausaineen käyttö johti voimakkaaseen kupari-ionien kompleksaatioon, jolloin pelkistysreaktiossa muodostui pinnasta hapettuneita n. 10 nm:n kokoisia kuparipartikkeleita. Oksidikerroksen todettiin alentavan suojausaineen pyrolyysilämpötilaa. Pyrolyysin yhteydessä kuparioksidikerroksen todettiin muuttuvan pääosin metalliseksi kupariksi ja sintrattujen jatkuvien kerrosten todettiin olevan puolijohteita. Kaliks[4]areeneillä pinnoitettuja kultapartikkeleita syntetisoitiin, ja niiden pintakemiaa säädettiin käyttämällä alkaanitiolien ja kaliksareenien seoksia. Voitiin osoittaa, että pintaan sidotut kaliksareenit kykenivät kompleksoimaan orgaanisia pyridiniumkationeita ja että kompleksaation kautta partikkelit aggregoituivat suuremmiksi kokonaisuuksiksi. Pinnalla olevien kaliksareenien kompleksointikykyä kyettiin säätämään muuttelemalla kaliksareenien ja alkaanitiolien tyyppiä ja suhteellista osuutta pintakerroksessa. Alkaanitiolilla suojatuista kultananopartikkeleista tehtiin muste, joka tulostettiin mustesuihkutulostimella paperille. Tulostetut kuviot sintrattiin sähköä johtaviksi kuvioiksi. Tulokset osoittivat, että kultananomusteilla voidaan tulostaa paperisubstraatille samanlaatuisia johtimia kuin lasisubstraatille

3D-suunnittelu esillepanoprosessin apuvälineenä

EVTEK-ammattikorkeakoulu Muotoiluinstituutti Viestinnän koulutusohjelma Graafinen suunnittelu Tekijä: Jani Pulkkinen Opinnäytetyön nimi: 3D-suunnittelu esillepanoprosessin apuvälineenä Vuosi: 2008 Sivumäärä: 32+2 Tämän opinnäytetyön tavoitteena on ollut uuden työkalun luominen, jolla elintarvikkeiden esillepanoja voidaan suunnitella kolmiulotteisesti. Mallinnoksen avulla on pyritty helpottamaan visualistin työtä esillepanojen suunnittelussa, rakentamisessa, sekä ideoiden läpiviennissä presentoinnin avulla. Työssä on käytetty Googlen SketchUp 3D-ohjelmaa, jonka ominaisuuksia on lisätty laajennoksilla siten, että kaupallisia tunnuslukuja voidaan kytkeä esillepanosuunnittelun tueksi. Työkalun pääasiallinen tehtävä on tuottaa myynnille havainnekuvia tulevista kampanjoista ja niihin liittyvistä tuotteiden esillepanoista. Havainnekuvat sijoitetaan valmiille taittopohjalle, josta ne tulostetaan ohjeistuksiksi kampanjaan liittyvillä oheistiedoilla varustettuna. Työkalun toimivuutta on testattu käytännössä siten, että yksi Stockmannin elintarvikeosastoista on suunniteltu Hullut Päivät-kampanjaan, tavoitteena selkeä, looginen ja visuaalisesti toimiva kokonaisuus. Samalla on tarkkailtu mallinnoksen vaikutuksia rakennusprosessiin, jossa on ollut osallisena useita toimijoita. Opinnäytetyön kirjallisessa osiossa arvioidaan menetelmän käytön sujuvuutta, mahdollisia jatkokehitysnäkymiä sekä ohjelmoinnista saatavaa lisäarvoa mallinnoksen kehittämisessä. Tavoitteena on luoda pysyvä toimintatapa mallintamisen ympärille. Avainsanat: 3D-mallintaminen, esillepano, kampanjasuunnittelu, ohjeistaminenEVTEK Institute of Arts and Design Degree Program(me): Bachelor`s degree, Adult Education Major: Graphic Design Supervisors: Arja Vuorio, Ale Torkkel Title: 3D-Design as a procedure in product displays Author(s): Jani Pulkkinen Year: 2008 Pages: 32 Abstract The target of this research was to solve, how effective 3D-program tool can be, when product displays are designed for department store. Designer must be able to sell ideas and share visions with forthcoming campaingns. Conferences and presentations for personnel is one sector in field of visual marketing. In a rapid changing sales department, usually three-dimensional planning is conceived as a slow and expensive method to make presentations. Thesis is based in case study, where Stockmann`s campaing called; "Hullut Päivät (grazy days)", was planned with Google`s freeware-program. The model was used as a platform to make pictures for construction of the Delicatess department. One of the essential features was the possibility to add sales attributes as an attachment to the model. This property was achieved by using Ruby Script -programming language. Material for presentations can be printed from templates developed for this project, and additionally make videopresentation with the same values. The conclusion of this thesis is that 3D-modeling is useful, when a multidisciplinary team has to be managed. Three-dimensional pictures made the department`s construction quicker, and in future, model can be easily updated and presented. Best results can be achieved when models and visual information can be shared intramural web by any part involved. Evolution of common product and furniture libraries enables adjustable and faster way to work. Keywords: three-dimensional design, displays, presentation, campaig

Turbulent viscosity and Lambda-effect from numerical turbulence models

Homogeneous anisotropic turbulence simulations are used to determine off-diagonal components of the Reynolds stress tensor and its parameterization in terms of turbulent viscosity and Lambda-effect. The turbulence is forced in an anisotropic fashion by enhancing the strength of the forcing in the vertical direction. The Coriolis force is included with a rotation axis inclined relative to the vertical direction. The system studied here is significantly simpler than that of turbulent stratified convection which has often been used to study Reynolds stresses. Certain puzzling features of the results for convection, such as sign changes or highly concentrated latitude distributions, are not present in the simpler system considered here.Comment: 3 pages, 2 figures, accepted for publication in Astronomische Nachrichte