Langevin Thermostat for Rigid Body Dynamics

We present a new method for isothermal rigid body simulations using the quaternion representation and Langevin dynamics. It can be combined with the traditional Langevin or gradient (Brownian) dynamics for the translational degrees of freedom to correctly sample the NVT distribution in a simulation of rigid molecules. We propose simple, quasi-symplectic second-order numerical integrators and test their performance on the TIP4P model of water. We also investigate the optimal choice of thermostat parameters.Comment: 15 pages, 13 figures, 1 tabl

Non-Hamiltonian dynamics in optical microcavities resulting from wave-inspired corrections to geometric optics

We introduce and investigate billiard systems with an adjusted ray dynamics that accounts for modifications of the conventional reflection of rays due to universal wave effects. We show that even small modifications of the specular reflection law have dramatic consequences on the phase space of classical billiards. These include the creation of regions of non-Hamiltonian dynamics, the breakdown of symmetries, and changes in the stability and morphology of periodic orbits. Focusing on optical microcavities, we show that our adjusted dynamics provides the missing ray counterpart to previously observed wave phenomena and we describe how to observe its signatures in experiments. Our findings also apply to acoustic and ultrasound waves and are important in all situations where wavelengths are comparable to system sizes, an increasingly likely situation considering the systematic reduction of the size of electronic and photonic devices.Comment: 6 pages, 4 figures, final published versio

Dynamics of leaf-and root-specific biomarkers during 1-year of litter decomposition

Root-specific and leaf-specific biomarkers have been used for decades to identify the origin of organic materials in soils and sediments. However, quantitative approaches require appropriate knowledge about the fate of these indicator molecules during degradation. To clarify this issue, we performed a 1-year incubation experiment with fine root and leaf material of six temperate tree species: European ash (Fraxinus excelsior), European beech (Fagus sylvatica), Oak spec. (Quercus spec.), Linden spec. (Tilia spec.), Norway spruce (Picea abies) and Scots pine (Pinus sylvatica). Only one molecule, x,16-dihydroxy hexadecanoic acid (x,16-C16), could be validated as a general leaf-specific biomarker for the set of all species. For roots, no general root biomarker was found. Ester-bound tricosanol (C23-OH) could be validated for five out of six species; 20-hydroxy eicosanoic acid (ωC20) could be validated for four out of six species, leaving Norway spruce without a suitable root biomarker. The results of this study suggest that the validity of leaf- and root-derived ester-bound lipids as biomarkers is highly species dependent and does not always coincide with previous findings. Concentrations of root- and leaf-derived ester-bound lipids did not stay constant within 1 year of degradation and changed without a linear trend. The change of concentrations seems to be highly species dependent. This might be due to a different structure and arrangement of the individual monomers in cutin and suberin per species, and, therefore, a different accessibility of bond cleaving enzymes. The usefulness of root and leaf biomarkers is context dependent. Our results suggest that general assumptions about litter input to forest soils solely based on biomarker analysis have to be considered carefully

Allelomimesis as universal clustering mechanism for complex adaptive systems

Animal and human clusters are complex adaptive systems and many are organized in cluster sizes $s$ that obey the frequency-distribution $D(s)\propto s^{-\tau}$. Exponent $\tau$ describes the relative abundance of the cluster sizes in a given system. Data analyses have revealed that real-world clusters exhibit a broad spectrum of $\tau$-values, $0.7\textrm{(tuna fish schools)}\leq\tau\leq 2.95\textrm{(galaxies)}$. We show that allelomimesis is a fundamental mechanism for adaptation that accurately explains why a broad spectrum of $\tau$-values is observed in animate, human and inanimate cluster systems. Previous mathematical models could not account for the phenomenon. They are hampered by details and apply only to specific systems such as cities, business firms or gene family sizes. Allelomimesis is the tendency of an individual to imitate the actions of its neighbors and two cluster systems yield different $\tau$ values if their component agents display different allelomimetic tendencies. We demonstrate that allelomimetic adaptation are of three general types: blind copying, information-use copying, and non-copying. Allelomimetic adaptation also points to the existence of a stable cluster size consisting of three interacting individuals.Comment: 8 pages, 5 figures, 2 table

Advanced 3D cell culture techniques in micro-bioreactors, Part II: Systems and applications

In this second part of our systematic review on the research area of 3D cell culture in micro-bioreactors we give a detailed description of the published work with regard to the existing micro-bioreactor types and their applications, and highlight important results gathered with the respective systems. As an interesting detail, we found that micro-bioreactors have already been used in SARS-CoV research prior to the SARS-CoV2 pandemic. As our literature research revealed a variety of 3D cell culture configurations in the examined bioreactor systems, we defined in review part one “complexity levels” by means of the corresponding 3D cell culture techniques applied in the systems. The definition of the complexity is thereby based on the knowledge that the spatial distribution of cell-extracellular matrix interactions and the spatial distribution of homologous and heterologous cell–cell contacts play an important role in modulating cell functions. Because at least one of these parameters can be assigned to the 3D cell culture techniques discussed in the present review, we structured the studies according to the complexity levels applied in the MBR systems

To dash or to dawdle: verb-associated speed of motion influences eye movements during spoken sentence comprehension

In describing motion events verbs of manner provide information about the speed of agents or objects in those events. We used eye tracking to investigate how inferences about this verb-associated speed of motion would influence the time course of attention to a visual scene that matched an event described in language. Eye movements were recorded as participants heard spoken sentences with verbs that implied a fast (“dash”) or slow (“dawdle”) movement of an agent towards a goal. These sentences were heard whilst participants concurrently looked at scenes depicting the agent and a path which led to the goal object. Our results indicate a mapping of events onto the visual scene consistent with participants mentally simulating the movement of the agent along the path towards the goal: when the verb implies a slow manner of motion, participants look more often and longer along the path to the goal; when the verb implies a fast manner of motion, participants tend to look earlier at the goal and less on the path. These results reveal that event comprehension in the presence of a visual world involves establishing and dynamically updating the locations of entities in response to linguistic descriptions of events

Neutrino Physics and Nuclear Axial Two-Body Interactions

We consider the counter-term describing isoscalar axial two-body currents in the nucleon-nucleon interaction, L1A, in the effective field theory approach. We determine this quantity using the solar neutrino data. We investigate the variation of L1A when different sets of data are used.Comment: 8 pages with 4 figures. To be published in the Proceedings of the Conference "Blueprints For The Nucleus: From First Principles to Collective Motion" held at Feza Gursey Institute, Istanbul, Turkey; May 17 -22, 200