Optically Controlled Stochastic Jumps of Individual Gold Nanorod Rotary Motors

Brownian microparticles diffusing in optical potential energy landscapes constitute a generic testbed for nonequilibrium statistical thermodynamics and has been used to emulate a wide variety of physical systems, ranging from Josephson junctions to Stirling engines. Here we demonstrate that it is possible to scale down this approach to nanometric length-scales by constructing a tilted washboard potential for the rotation of plasmonic gold nanorods. The potential depth and tilt can be precisely adjusted by modulating the light polarization. This allows for a gradual transition from continuous rotation to discrete stochastic jumps, which are found to follow Kramers dynamics in excellent agreement with stochastic simulations. The results widen the possibilities for fundamental experiments in statistical physics and provide new insights in how to construct light-driven nanomachines and multifunctional sensing elements.Comment: 6 pages, 4 figure

Schottky barrier formation and band bending revealed by first principles calculations

An atomistic insight into potential barrier formation and band bending at the interface between a metal and an n-type semiconductor is achieved by ab initio simulations and model analysis of a prototype Schottky diode, i.e., niobium doped rutile titania in contact with gold (Au/Nb:TiO$_2$). The local Schottky barrier height is found to vary between 0 and 1.26 eV depending on the position of the dopant. The band bending is caused by a dopant induced dipole field between the interface and the dopant site, whereas the pristine Au/TiO$_2$ interface does not show any band bending. These findings open the possibility for atomic scale optimization of the Schottky barrier and light harvesting in metal-semiconductor nanostructures

Realizing strong light-matter interactions between single nanoparticle plasmons and molecular excitons at ambient conditions

Realizing strong light-matter interactions between individual 2-level systems and resonating cavities in atomic and solid state systems opens up possibilities to study optical nonlinearities on a single photon level, which can be useful for future quantum information processing networks. However, these efforts have been hampered by the unfavorable experimental conditions, such as cryogenic temperatures and ultrahigh vacuum, required to study such systems and phenomena. Although several attempts to realize strong light-matter interactions at room-temperature using so-called plasmon resonances have been made, successful realizations on the single nanoparticle level are still lacking. Here, we demonstrate strong coupling between plasmons confined within a single silver nanoprism and excitons in molecular J-aggregates at ambient conditions. Our findings show that the deep subwavelength mode volumes, $V$, together with high quality factors, $Q$, associated with plasmons in the nanoprisms result in strong coupling figure-of-merit -- $Q/\sqrt{V}$ as high as $\sim6\times10^{3}$~$\mu$m$^{-3/2}$ -- a value comparable to state-of-art photonic crystal and microring resonator cavities, thereby suggesting that plasmonic nanocavities and specifically silver nanoprisms can be used for room-temperature quantum optics

From sequence to structure to networks

A report on the 7th European Conference on Computational Biology (ECCB), Cagliari, Italy, 22-26 September 2008

Superconductive Phonon Anomalies in High-TcT_c Cuprates

We consider the effects on phonon dynamics of spin-lattice coupling within the slave-boson mean-field treatment of the extended $t$-$J$ model. With no additional assumptions the theory is found to give a semi-quantitative account of the frequency and linewidth anomalies observed by Raman and neutron scattering for the 340$cm^{-1}$ $B_{1g}$ phonon mode in $YBa_2Cu_3O_7$ at the superconducting transition. We discuss the applicability of the model to phonon modes of different symmetries, and report a connection to spin-gap features observed in underdoped YBCO. The results suggest the possibility of a unified understanding of the anomalies in transport, magnetic and lattice properties.Comment: heavily revised version of previous paper, including systematic treatment of effect of $t$ term, coupling constant derivation and calculation of phonon linewidth broadening. Revised Figs. 3 and 4 still only available by sending fax # to [email protected]

Encountering abused animals and humans : the prevalence of a plan of action at small animal clinics in Sweden

Att våld i nära relationer korrelerar med våld mot djur är väl belagt i internationell forskning och är ett växande forskningsområde inom Sverige. Det anses finnas vissa svårigheter att från klinikernas sida inkludera djurägares levnadsförhållanden i anamnestagningen, då djurägares välfärd inte är klinikens primära ansvarsområde. Det kan dock ge viktig information som bidrar till att kartlägga djurets hemmiljö. Att anmäla djurägare som missköter sina djur, även om det är oavsiktligt, anses också vara en allvarlig åtgärd. Djursjukvården rekommenderas att följa humansjukvårdens modell och utarbeta en handlingsplan, där lämpliga åtgärder vid misstanke om vanvård och våld mot djur listas. Att utbilda personal både i våldets mekanismer och strategier för att hantera utsatta människor och djur uppmuntras. Syftet med studien var att undersöka hur utbrett arbetet med handlingsplaner är på svenska smådjurskliniker, samt att undersöka klinikernas inställning till att vidta förebyggande åtgärder inför situationer där vanvård eller våld mot djur misstänks. Vidare syftade studien till att utreda klinikernas benägenhet att agera när de ställs inför en sådan situation. Utöver enkätstudien har även svensk och internationell forskning granskats utifrån ett övergripande perspektiv för att ge en förståelse för ämnet. Våldets inverkan på utsatta människor, utsatta djur och djurhälsopersonal som i sin yrkesutövning möter utgör huvudfokus, men även aktuell politik, juridik och samhällssyn berörs. För att få svar på frågeställningarna genomfördes en enkätundersökning (Bilaga 1) i vilken 13 av Sveriges större smådjurskliniker deltog. En anställd per klinik svarade. Inkomna svar sammanställdes och diskuterades utifrån svensk och internationell forskning inom området samt tillämpbar lagstiftning. Resultatet visade att sju av 13 kliniker hade en fastställd handlingsplan gällande ärenden som rör vanvård eller våld mot djur. Totalt hade nio kliniker under det senaste året gjort anmälningar angående missförhållanden i djurhållningen till antingen länsstyrelse eller polis, däribland samtliga sju kliniker med handlingsplan. Utöver detta hade två kliniker en handlingsplan inför situationer där människor misstänks utsättas för våld och sex kliniker tillhandahöll information om sambandet mellan våld mot djur och våld i nära relationer till besökare. En klinik hade anmält oro för barns situation till Socialtjänsten. .The correlation between animal abuse and domestic violence is attested through numerous studies internationally but has rather recently gained greater attention in Sweden. The general opinion is that there are some difficulties with getting veterinary clinics to include the living circumstances of the owner into the anamnesis, since the clinics’ primary field of responsibility is animals’ health status, rather than that of the owners. However, this information would also contribute in giving a considerably more accurate picture of the animals’ living conditions. There also seems to be a slight resistance to report anything less than major animal neglect or abuse to the authorities. Veterinary clinics are advised to adopt the method applied in the human healthcare system, and develop a plan of action, wherein the interventions regarding suspected neglect and violence against animals would be resolved. It is also encouraged to educate the personnel in the proceedings of violence, as well as in strategies to take care of individuals in an exposed position, both humans and animals. The aim of this survey was to assess to which degree, if at all, Swedish small animal veterinary clinics make use of pre-written plans of action and what preventative measures they have applied in preparation to facing a situation where suspicions of violence arise. Furthermore, the survey was to answer whether the clinics would or would not act in these situations. In order to provide some insight in the subject of animal abuse and domestic violence a study of literature was conducted, with the main focus comprised to abused pet owners, abused animals and the animal health personnel. However, political, legal and societal factors are also discussed in relation to violence. Questions about the clinics tendency to report abuse and the structure of the decision-making process were asked in a web based poll (Attachment 1) to which 13 major clinics responded. The answers were compiled and evaluated against national and international research and Swedish legislation. The result shows that seven of the 13 clinics have a plan of action regarding animal abuse and neglect prepared. The result also states that every clinic which had a plan of action reported animal owners to the authorities due to neglect or abuse. However, of the six clinics lacking such a plan, only two made reports about inadequate animal care. Concerning the aspect of human victims of domestic abuse, fewer clinics had action plans. Six clinics provided information about the link between animal abuse and domestic violence, while only two clinics had action plans equivalent to those described above. One clinic had, on one occasion, reported concerns about the wellbeing of children to the authorities

Sensing (un)binding events via surface plasmons: Effects of resonator geometry

The resonance conditions of localized surface plasmon resonances (LSPRs) can be perturbed in any number ways making plasmon nanoresonators viable tools in detection of e.g. phase changes, pH, gasses, and single molecules. Precise measurement via LSPR of molecular concentrations hinge on the ability to confidently count the number of molecules attached to a metal resonator and ideally to track binding and unbinding events in real-time. These two requirements make it necessary to rigorously quantify relations between the number of bound molecules and response of plasmonic sensors. This endeavor is hindered on the one hand by a spatially varying response of a given plasmonic nanosensor. On the other hand movement of molecules is determined by stochastic effects (Brownian motion) as well as deterministic flow, if present, in microfluidic channels. The combination of molecular dynamics and the electromagnetic response of the LSPR yield an uncertainty which is little understood and whose effect is often disregarded in quantitative sensing experiments. Using a combination of electromagnetic finite-difference time-domain (FDTD) calculations of the plasmon resonance peak shift of various metal nanosensors (disk, cone, rod, dimer) and stochastic diffusion-reaction simulations of biomolecular interactions on a sensor surface we clarify the interplay between position dependent binding probability and inhomogeneous sensitivity distribution. We show, how the statistical characteristics of the total signal upon molecular binding are determined. The proposed methodology is, in general, applicable to any sensor and any transduction mechanism, although the specifics of implementation will vary depending on circumstances. In this work we focus on elucidating how the interplay between electromagnetic and stochastic effects impacts the feasibility of employing particular shapes of plasmonic sensors for real-time monitoring of individual binding reactions or sensing low concentrations - which characteristics make a given sensor optimal for a given task. We also address the issue of how particular illumination conditions affect the level of uncertainty of the measured signal upon molecular binding

DeepSig: Deep learning improves signal peptide detection in proteins

Motivation: The identification of signal peptides in protein sequences is an important step toward protein localization and function characterization. Results: Here, we present DeepSig, an improved approach for signal peptide detection and cleavage-site prediction based on deep learning methods. Comparative benchmarks performed on an updated independent dataset of proteins show that DeepSig is the current best performing method, scoring better than other available state-of-the-art approaches on both signal peptide detection and precise cleavage-site identification. Availability and implementation: DeepSig is available as both standalone program and web server at https://deepsig.biocomp.unibo.it. All datasets used in this study can be obtained from the same website

Complete genome sequence of the broad-host-range Paenibacillus larvae phage phiIBB_Pl23

Paenibacillus larvae is a Gram-positive bacterium that causes American foulbrood, an important disease in apiculture. We report the first complete genome sequence of a P. larvae phage, phiIBB_Pl23, isolated from a hive in northern Portugal. This phage belongs to the family Siphoviridae.A. O. and L.D.R.M. acknowledge the FCT (Fundacao para a ciencia e a tecnologia) grants SFRH/BPD/69356/2010 and SFRH/BD/66166/2009, respectively

Advantages of combined transmembrane topology and signal peptide prediction—the Phobius web server

When using conventional transmembrane topology and signal peptide predictors, such as TMHMM and SignalP, there is a substantial overlap between these two types of predictions. Applying these methods to five complete proteomes, we found that 30–65% of all predicted signal peptides and 25–35% of all predicted transmembrane topologies overlap. This impairs predictions of 5–10% of the proteome, hence this is an important issue in protein annotation