Depletion effects and loop formation in self-avoiding polymers

Langevin dynamics is employed to study the looping kinetics of self-avoiding polymers both in ideal and crowded solutions. A rich kinetics results from the competition of two crowding-induced effects: the depletion attraction and the enhanced viscous friction. For short chains, the enhanced friction slows down looping, while, for longer chains, the depletion attraction renders it more frequent and persistent. We discuss the possible relevance of the findings for chromatin looping in living cells.Comment: 4 pages, 3 figure

Role of Secondary Motifs in Fast Folding Polymers: A Dynamical Variational Principle

A fascinating and open question challenging biochemistry, physics and even geometry is the presence of highly regular motifs such as alpha-helices in the folded state of biopolymers and proteins. Stimulating explanations ranging from chemical propensity to simple geometrical reasoning have been invoked to rationalize the existence of such secondary structures. We formulate a dynamical variational principle for selection in conformation space based on the requirement that the backbone of the native state of biologically viable polymers be rapidly accessible from the denatured state. The variational principle is shown to result in the emergence of helical order in compact structures.Comment: 4 pages, RevTex, 4 eps figure

REMOTE SENSING METHODS FOR THE INVESTIGATION OF THE EVOLUTION AND DYNAMICS OF ALPINE LANDSCAPES

Whilst the effects of present-day climate change are apparent in many environmental systems, much less is known about its impact upon the geomorphic systems characteristic of Alpine environments. This is an important knowledge gap because of the potential vulnerability of Alpine landscapes. The gap exists for two primary reasons: (1) observing climate forcing is challenging because it is manifest over timescales of decades to centuries, over which timescale geomorphic data are commonly scarce; and (2) the geomorphic response of landscapes to climate change can be complex, reflecting both spatially differential sensitivities to climate forcing and the effects of landscape heritage associated with historical glacial activity. Nonetheless, there is a consensus in the scientific community about the potentially high sensitivity of Alpine regions to climate change, because of the vulnerability of permafrost, glacial and nival processes to changes in atmospheric temperature and precipitation and the large amount of sediment stored on the associated hillsides. One approach to addressing this knowledge gap is to harness the power of remote sensing. A number of active and passive remote sensing methods could be employed for the reconstruction and monitoring of both whole landscapes and individual landforms. This Thesis aims to use such approaches to quantify the geomorphic dynamics of high mountain areas at the timescale of decades and so in the context of recent and rapid climate warming. It does so recognizing that both endogenous (landscape legacy) and exogenous (climatic forcing) processes may matter. To support this primary aim, a secondary aim arises: the evaluation of the potential of a number of remote sensing techniques for landscape and landform monitoring at multiple temporal and spatial scales. Thus this Thesis also tests in an Alpine setting the geomorphological potential of photogrammetric methods, using both aerial and hand-held sensors and both traditional and the innovative Structure-from-Motion processing approaches, and Terrestrial Laser Scanner techniques. The Thesis shows that remote sensing approaches prove to be an advantageous approach for a number of scales of application. In particular, over large spatial extents and in the case of decadal scale climate forcing of Alpine landscapes, photogrammetry was found to be capable of quantifying process rates within the limits of detection determined by the resolution of historical imagery. The information unlocked from aerial archives reveals distinct geomorphic responses to cold and warm periods and to changes in rates of precipitation and snow cover. Nonetheless, whilst enhanced sediment production is observed locally, evidence suggest a weak propagation of climate change signals through the landscape due to impeded connection to the river system and/or sediment transport capacity limitation. -- Bien que les effets des changements climatiques actuels soient visibles dans de nombreux systèmes environnementaux, un manque de connaissances des impacts sur les paysages alpins persiste. Cette lacune existe pour deux raisons principales : (1) l'observation du forçage climatique représente un défi, car ses conséquences se manifestent sur des périodes de plusieurs décennies, voire des siècles, pour lesquels les données géomorphologiques sont généralement rares ; et (2) la réaction du paysage aux changements climatiques peut être complexe, reflétant à la fois des sensibilités différentes au niveau spatial et les effets du patrimoine paysager, comme par exemple son histoire glaciaire. Néanmoins, il existe un consensus dans la communauté scientifique à propos de la haute sensibilité potentielle des régions alpines au changement climatique, en raison de la vulnérabilité du pergélisol et des processus glaciaires et neigeux aux changements de température atmosphérique et des précipitations et en raison de la grande quantité de sédiments stockés sur les versants alpins. Une stratégie pour aborder ces problématiques s'appuie sur le potentiel de la télédétection. Une série de méthodes de télédétection active et passive peuvent être utilisées pour reconstruire et surveiller le paysage entier et les éléments individuels qui le composent. Cette thèse vise l'application de ces approches pour quantifier les dynamiques géomorphologiques des paysages de haute montagne à l'échelle des décennies, et donc dans le contexte du réchauffement climatique récent et actuel. Cela est mis en pratique par la reconnaissance de l'importance des processus endogènes (héritage du paysage) et exogènes (forçage climatique). Le soutien à cet objectif en soulève un deuxième : l'évaluation du potentiel d'un certain nombre de techniques de télédétection pour le monitorage du relief et de ses formes géomorphologiques à plusieurs échelles temporelles et spatiales. Ainsi, cette thèse teste le potentiel des méthodes de photogrammétrie, en utilisant à la fois des senseurs aéroportés et portatifs et des approches de traitements traditionnels et innovants, et du balayage laser terrestre pour la recherche géomorphologique alpine. Les résultats obtenus montrent que les approches de télédétection se révèlent avantageuses pour des nombreuses échelles d'application. En particulier, sur de grandes étendues spatiales et dans le contexte du forçage climatique du paysage alpin, la photogrammétrie aérienne d'archive se montre appropriée pour la quantification des taux des processus dans les limites de détection déterminées par la résolution des photographies historiques. Les résultats démontrent l'existence d'une réponse géomorphologique distincte pour des périodes froides ou chaudes, ainsi que selon les variations des taux de précipitations et de couverture de neige. Néanmoins, alors qu'une production accrue de sédiments est observée localement, des évidences suggèrent une faible propagation des signaux du changement climatique à travers le paysage. Les raisons semblent être une faible contribution des versants au réseau fluvial et/ou une capacité de transport des sédiments limitée. -- Obwohl die Auswirkungen des aktuellen Klimawandels in zahlreichen Umweltsystemen beobachtet wurden, sind die Kenntnisse dieser Auswirkungen auf alpine Landschaften immer noch ungenügend. Diese Lücke existiert aus folgenden Gründen: (1) Das Beobachten klimatischer Auswirkungen auf alpine geomorphologische Prozesse stellt eine grosse Herausforderung dar, da diese sich über eine Zeitspanne von mehreren Jahrzehnten bis Jahrhunderten bemerkbar machen können, für die meist nur wenige geomorphologische Daten zur Verfügung stehen. (2) Durch die unterschiedlichen Empfind- lichkeiten verschiedener geomorphologischer Landschaftselemente sowie durch den grossen Einfluss des landschaftlichen Erbes, wie zum Beispiel der historischen Gletschertätigkeit, reagieren alpine Landschaftsentwicklungsprozesse sehr komplex auf Veränderungen des Klimas. Nichtsdestotrotz, auf- grund der hohen Empfindlichkeit des Permafrosts und der Gletscher- und Schneeprozesse gegenüber Veränderungen der atmosphärischen Temperatur und der Niederschlagsmenge sowie der grossen Menge an Sedimenten die an den Alpenhängen abgelagert werden und wurden, herrscht in der wis- senschaftlichen Gemeinschaft ein breiter Konsens über die potentielle hohe Sensibilität der alpinen geomorphologischen Systeme in Bezug auf den zu erwartenden Klimawandel. Fernerkundung bietet ein hohes Potential, um die geomorphologische Sensibilität zu erkunden. Aktive und passive Fernerkundungsmethoden können genutzt werden, um gesamte Landschaften sowie ihre einzelnen geomorphologischen Elemente historisch zu rekonstruieren und kontinuierlich zu überwachen. Die vorliegende Dissertation zielt auf die Anwendung dieser Ansätze, um die geomorpho- logische Dynamik der hochalpinen Landschaft über Jahrzehnte, und somit im Kontext der jüngsten Klimaerwärmung, zu quantifizieren. Der hier dargestellte Ansatz fokussiert vor allem auf die Bedeutung der endogenen (landschaftliches Erbe) und exogenen (klimatische Einflüsse) Prozesse. Die Umsetzung dieses primären Ziels zieht ein sekundäres Ziel mit sich: Die Bewertung des Potenzials einer Reihe von Fernerkundungsmethoden für das Monitoring von Landschaften und ihrer geomorphologischen For- men auf mehreren rüumlichen und zeitlichen Skalen. Damit wird das Potenzial photogrammetrischer Methoden, insbesondere luftgestützter und tragbarer Sensoren in Kombination mit traditionellen und innovativen "Structure-from-Motion" Ansätzen, sowohl auch terrestrischen Laserscanning Techniken für die alpine geomorphologische Forschung getestet. Die Ergebnisse zeigen, dass die hier dargestellten Fernerkundungsansätze für eine breite Reihe von Anwendungsskalen vorteilhaft sind. Die Archiv-Luftphotogrammmetrie ist besonders für die Quan- tifizierung der Auswirkungen des Klimawandels auf geomorphologische Prozesse in grossen Land- schaftsausschnitten geeignet. Die Auflösung der historischen Luftbilder bestimmt die Detektionsgrenze dieser Prozesse. Die aus den Luftarchiven ermittelten Informationen zeigen, dass kalte und warme Klimaphasen, sowie Variationen der Niederschlagsmenge und der Schneedeckenmächtigkeit unter- schiedliche Auswirkungen auf geomorphologische Prozesse haben. Obwohl ein lokaler Anstieg der Sedimentproduktion beobachtet werden konnte, konnten nur geringe Anzeichen einer Ausbreitung dieser Klimawandelsignale in der Landschaft beobachtet werden. Die Gründe hierfür scheinen der geringe Beitrag der untersuchten Berghänge zum Gesamtwasserabfluss und/oder die beschränkte Sedimenttransportfähigkeit zu sein. -- Nonostante gli effetti del cambiamento climatico attuale siano evidenti in molti sistemi ambientali, una conoscenza deficitaria perdura riguardo il suo impatto sui paesaggi alpini. Tale lacuna esiste per due principali ragioni: (1) gli effetti del cambiamento climatico sono difficili da osservare, in quanto manifesti su scale temporali di decenni, o persino secoli, per le quali prevale una scarsità di dati geomorfologici esaustivi; e (2) la reazione del paesaggio a tali cambiamenti può essere complessa e riflettere al contempo delle sensibilità spaziali differenti e gli effetti del patrimonio paesaggistico, come ad esempio la cronistoria glaciale. Tuttavia, vi è un consenso nella comunità scientifica riguardo l'ele- vata sensibilità delle regioni alpine ai cambiamenti climatici, a causa della vulnerabilità di permafrost e processi glaciali e nevosi ai cambiamenti di temperatura atmosferica e di precipitazioni, oltre che all'ampio stoccaggio di sedimenti concentrato sui pendii alpini. Una strategia per colmare questa lacuna di conoscenza può essere l'avvalersi del potenziale delle tecniche di telerilevamento. Vari metodi di telerilevamento attivo e passivo possono essere impiegati per ricostruire e monitorare il paesaggio ed i singoli elementi che lo compongono. Questa tesi si propone di utilizzare tali metodi per quantificare le dinamiche geomorfologiche nelle regioni di alta montagna a scala temporale decennale, e quindi nel contesto del riscaldamento climatico recente e attuale. In tale approccio viene riconosciuta l'importanza dei processi di tipo endogeno (di eredità paesaggistica) ed exogeno (climatici). A sostegno di questo obiettivo primario, una seconda finalità si pone: lo sviluppo e la valutazione di diverse tecniche di telerilevamento per il monitoraggio dei rilievi alpini e delle loro forme geomorfologiche, a più scale temporali e spaziali. Pertanto, questa tesi mette alla prova metodi di fotogrammetria, utilizzando al contempo sensori aeroportati e portatili ed approcci tradizionali ed innovativi (come l'emergente Structure-from-Motion), e tecniche di scansione laser per la ricerca geomorfologica in scenari alpini. I risultati ottenuti dimostrano come gli approcci di telerilevamento rappresentino una risorsa efficace e vantaggiosa per una vasta gamma di applicazioni. In particolare, ad ampia scala spaziale e nel contesto di cambiamento climatico nelle regioni alpine, la fotogrammetria aerea d'archivio si è dimostrata appropriata per la quantificazione dei processi geomorfologici entro limiti di rilevamento determinati dalla risoluzione delle immagini storiche stesse. I risultati rivelano una reazione geomorfica distinta a periodi di caldo e freddo, oltre che a variazioni di precipitazioni e copertura nevosa. Ciononostante, malgrado un accrescimento della produzione sedimentaria sia presente a scala locale, la propagazione dei segnali di cambiamento climatico attraverso il paesaggio appare debole. La ragione risiede nello scarso contributo dei versanti al sistema fluviale e/o a limitate capacità di trasporto di sedimenti

Surface spin-flop and discommensuration transitions in antiferromagnets

Phase diagrams as a function of anisotropy $D$ and magnetic field $H$ are obtained for discommensurations and surface states for an antiferromagnet in which $H$ is parallel to the easy axis, by modeling it using the ground states of a one-dimensional chain of classical XY spins. A surface spin-flop phase exists for all $D$, but the interval in $H$ over which it is stable becomes extremely small as $D$ goes to zero. First-order transitions, separating different surface states and ending in critical points, exist inside the surface spin-flop region. They accumulate at a field $H'$ (depending on $D$) significantly less than the value $H_{SF}$ for a bulk spin-flop transition. For $H' < H < H_{SF}$ there is no surface spin-flop phase in the strict sense; instead, the surface restructures by, in effect, producing a discommensuration infinitely far away in the bulk. The results are used to explain in detail the phase transitions occurring in systems consisting of a finite, even number of layers.Comment: Revtex 17 pages, 15 figure

Standard methods for creating digital skeletal models using structure-from-motion photogrammetry.

OBJECTIVES: This article assesses best practices for producing 3D digital cranial models through structure-from-motion (SfM) photogrammetry, and whether the metric accuracy and overall presentation of photogrammetric models are comparable to physical crania. It is intended to present a user-friendly standard method of creating accurate digital skeletal models using Agisoft PhotoScan. MATERIALS AND METHODS: Approximately 200 photographs were taken of three different crania, and were separated into series consisting of 50, 75, 100, 150, and approximately 200 photos. Forty-five cranial models were created using different photo series and a variety of PhotoScan settings. These models were assessed based on defined qualitative criteria, and model measurement estimates were compared with physical skeletal measurements using Bland-Altman plots. RESULTS: The majority of all models (37/45) produced measurement estimates with mean differences of 2 mm or less regardless of PhotoScan settings, and therefore demonstrated high levels of agreement with the physical measurements. Models created with 150 photographs and on "high" PhotoScan settings scored the highest in terms of qualitative appearance in the shortest amount of time. DISCUSSION: In PhotoScan, it is recommended to create cranial models using 150 photographs and "high" settings; this produces digital cranial models that are comparable to physical crania in both appearance and proportion. SfM photogrammetry is a convenient, noninvasive, and rapid 3D modeling tool that can be used in almost any setting to produce digital models, and following the guidelines established here will ensure that these models are metrically accurate

Structure from motion (SFM) photogrammetry

Topographic data measurement is a fundamental aspect of many geomorphic research applications, particularly those including landform monitoring and investigation of changes in topography. However, most surveying techniques require relatively expensive technologies or specialized user supervision. Structure from Motion (SfM) photogrammetric technology lightens both these constraints by allowing the use of consumer grade digital cameras and highly automated data processing, which can be free to use. SfM photogrammetry therefore offers the possibility of fast, automated and low-cost acquisition of 3-D data, which has inevitably created great interest amongst the geomorphological community. In this contribution, the basic concepts of SfM photogrammetry are presented, whilst recognising its heritage. A few examples are employed to illustrate the potential of SfM applications for geomorphological research. In particular, SfM photogrammetry offers to geomorphologists a tool for high-resolution characterisation of 3-D forms at a range of scales and for change detection purposes. The high level of automation of SfM data processing creates both opportunities and threats, particularly because user control tends to focus upon the final product visually rather than upon inherent data quality. Accordingly, this contribution seeks to guide potential new users in successfully applying SfM for a range of geomorphic studies

Is SfM photogrammetry really the tool we've waited 30 years for?

SFM photogrammetry has evolved rapidly in the last few years, to the point where it is beginning to surpass terrestrial laser scanning for capturing 3-D models of natural surfaces. The ability to generate high resolution digital terrain models using just a consumer grade digital camera, or even a smart phone, is an important advance. The fact that this can be achieved at a range of scales and resolutions and from a variety of platforms, whilst using software which is freely available, appears almost incredible

Surface spin-flop transition in a uniaxial antiferromagnetic Fe/Cr superlattice induced by a magnetic field of arbitrary direction

We studied the transition between the antiferromagnetic and the surface spin-flop phases of a uniaxial antiferromagnetic [Fe(14 \AA)/Cr(11 \AA]$_{\rm x20}$ superlattice. For external fields applied parallel to the in-plane easy axis, the layer-by-layer configuration, calculated in the framework of a mean-field one-dimensional model, was benchmarked against published polarized neutron reflectivity data. For an in-plane field $H$ applied at an angle $\psi \ne 0$ with the easy axis, magnetometry shows that the magnetization $M$ vanishes at H=0, then increases slowly with increasing $H$. At a critical value of $H$, a finite jump in $M(H)$ is observed for $\psi<5^{\rm o}$, while a smooth increase of $M$ $vs$ $H$ is found for $\psi>5^{\rm o}$. A dramatic increase in the full width at half maximum of the magnetic susceptibility is observed for $\psi \ge 5^{\rm o}$. The phase diagram obtained from micromagnetic calculations displays a first-order transition to a surface spin-flop phase for low $\psi$ values, while the transition becomes continuous for $\psi$ greater than a critical angle, $\psi_{\rm max} \approx 4.75^{\rm o}$. This is in fair agreement with the experimentally observed results.Comment: 24 pages, 7 figure

Hydrodynamics and filtering of knotted ring polymers in nanochannel

We study the hydrodynamic transport of knotted ring polymers through modulated channels, establishing that the transport velocity is strongly dependent on the ring topology for Peclet numbers smaller than unity. As soon as convection dominates, transport properties become insensitive to the presence and type of knots. We identify two distinct modes of transport, corresponding to the motion being led by the knotted or unknotted portions of the ring, most surprisingly without impact on separation efficiency. The modes can be selected by the channel geometry, and this could be harnessed to design nanofluidic devices for the continuous topological sorting of entangled biopolymers