Crowding Effects in Vehicular Traffic

While the impact of crowding on the diffusive transport of molecules within a cell is widely studied in biology, it has thus far been neglected in traffic systems where bulk behavior is the main concern. Here, we study the effects of crowding due to car density and driving fluctuations on the transport of vehicles. Using a microscopic model for traffic, we found that crowding can push car movement from a superballistic down to a subdiffusive state. The transition is also associated with a change in the shape of the probability distribution of positions from a negatively-skewed normal to an exponential distribution. Moreover, crowding broadens the distribution of cars’ trap times and cluster sizes. At steady state, the subdiffusive state persists only when there is a large variability in car speeds. We further relate our work to prior findings from random walk models of transport in cellular systems.     

Role of refractory period in homoclinic models of neural synchronization

We study the properties of a homoclinic model of neuron by introducing a suitable one-dimensional map. We show that the system is characterized by a response time to external signals which is a decreasing function of the signal strength, in contrast to excitable models whose response time is signal-independent. In a one-dimensional array of these systems with bidirectional coupling, we observe a sudden transition to a synchronized state at a certain value of the coupling strength. The transition occurs when the response time of a site to the signals of the adjacent sites is of the order of refractory time. Near the transition, we find an intermittent behavior due to the competition between a turbulent and a synchronized state. The observed behavior distinguishes homoclinic systems from excitable systems.     

Simultaneous modeling of phase and calorimetric behavior in an amphiphilic peptide/phospholipid model membrane

Differential scanning calorimetry (DSC) experiments have been performed on the amphiphilic peptide/1,2-bis(perdeuteriopalmitoyl)-sn-glycero-3-phosphocholine system for which partial phase diagrams have been measured by deuterium nuclear magnetic resonance. The solute concentration dependence of the transition enthalpy in such systems is often interpreted in terms of an annulus of lipid withdrawn, by the solvent, from participation in the transition while the bulk lipid melts with its fully enthalpy. This idea is equivalent to postulating ideal mixing between the lipid and the peptide/lipid complex, and there is little justification for such an assumption. Adaptation of regular solution theory to this system demonstrates that the peptide concentration dependence of the transition enthalpies can be incorporated into a thermodynamic model which reproduces the observed phase behavior fairly well without postulating that a complexing annulus of lipid around the peptide be withdrawn from participating in the chain-melting transition. The model parameters determined by simultaneous fitting of the phase behavior and transition enthalpies are used to simulate the DSC scan shapes. The asymmetry of the calorimetric scans for chi 2 less than or equal to 0.02 is reproduced by the model, but a broad component observed for higher concentration is not. In light of the results presented here, previous analyses of the calorimetric behavior of two-component systems in terms of symmetric transitions which do not account for the possible extent of a region of two-phase equilibrium must be questioned.     

Behavior of Early Warnings near the Critical Temperature in the Two-Dimensional Ising Model

Among the properties that are common to complex systems, the presence of critical thresholds in the dynamics of the system is one of the most important. Recently, there has been interest in the universalities that occur in the behavior of systems near critical points. These universal properties make it possible to estimate how far a system is from a critical threshold. Several early-warning signals have been reported in time series representing systems near catastrophic shifts. The proper understanding of these early-warnings may allow the prediction and perhaps control of these dramatic shifts in a wide variety of systems. In this paper we analyze this universal behavior for a system that is a paradigm of phase transitions, the Ising model. We study the behavior of the early-warning signals and the way the temporal correlations of the system increase when the system is near the critical point.     

Criticality found in a model for orientational ordering of protein arrays

MC-PSRG analysis allowed us to reduce criticalities A, B, and C found in the poker chip model, respectively, to ones of the Ising universality, of the 3-state Potts universality, and of the KT-like phase. We note that not only the KT-like phase but also the Ising and 3-state Potts universality have been predicted to appear in the generalized 6-state clock model. We expect that the criticality inherent in actual protein array systems, whose Hamiltonians might be more complex than those of the poker chip model, can also be reduced to the criticality clarified with the aid of the naive models. However, we have to direct our attention to nonuniversal behavior like criticality C. Several two-dimensional systems having the two-component order parameter exhibit nonuniversal critical behavior, whose critical exponents do not coincide with those for the XY model despite a coincidence in the number of order parameter components (17, 20, 25).     

Controlling composition of coexisting phases via molecular transitions

Phase separation and transitions among different molecular states are ubiquitous in living cells. Such transitions can be governed by local equilibrium thermodynamics or by active processes controlled by biological fuel. It remains largely unexplored how the behavior of phase-separating systems with molecular transitions differs between thermodynamic equilibrium and cases in which the detailed balance of the molecular transition rates is broken because of the presence of fuel. Here, we present a model of a phase-separating ternary mixture in which two components can convert into each other. At thermodynamic equilibrium, we find that molecular transitions can give rise to a lower dissolution temperature and thus reentrant phase behavior. Moreover, we find a discontinuous thermodynamic phase transition in the composition of the droplet phase if both converting molecules attract themselves with similar interaction strength. Breaking the detailed balance of the molecular transition leads to quasi-discontinuous changes in droplet composition by varying the fuel amount for a larger range of intermolecular interactions. Our findings showcase that phase separation with molecular transitions provides a versatile mechanism to control properties of intracellular and synthetic condensates via discontinuous switches in droplet composition.     

Head-on collisions of waves in an excitable FitzHugh-Nagumo system: a transition from wave annihilation to classical wave behavior

For the particular case of an excitable FitzHugh-Nagumo system with diffusion, we investigate the transition from annihilation to crossing of the waves in the head-on collision. The analysis exploits the similarity between the local and the global phase portraits of the system. We find that the transition has features typical of the nucleation theory of first-order phase transitions, and may be understood through purely geometrical arguments. In the case of periodic boundary conditions, the transition is an infinite-dimensional analog of the creation and the vanishing of limit cycles via a homoclinic Andronov bifurcation. Both before and after the transition, the behavior of a single cell continues to be typical for excitable systems: a stable equilibrium state, and a threshold above which an excitation pulse can be induced. The generality and qualitative character of our argument shows that the phenomenon described can be observed in excitable systems well beyond the particular case presented here.     

Effects of pentanol isomers on the phase behavior of phospholipid bilayer membranes

Differential scanning calorimetry (DSC) was used to analyze the thermotropic phase behavior of dipalmitoylphosphatidylcholine (DPPC) bilayers in the presence of pentanol isomers. The concentration of each pentanol isomer needed to induce the interdigitated phase was determined by the appearance of a biphasic effect in the main transition temperatures, the onset of a hysteresis associated with the main transition from the gel-to-liquid crystalline phase, and the disappearance of the pretransition. Lower threshold concentrations were found to correlate with isomers of greater alkyl chain length while branching of the alkyl chain was found to increase biphasic behavior. The addition of a methyl group to butanol systems drastically decreased threshold concentrations. However, as demonstrated in the DPPC/neopentanol system, branching of the alkyl chain away from the -OH group lowers the threshold concentration while maintaining a biphasic effect.     

Stochastic model of domain kinetics in biological membranes

A stochastic storage model based on the behavior of macroscopic variables of the system is used to describe the kinetics of raft-like domains in biological membranes. For a simple output model, we examine the features of the system behavior corresponding to the noise-induced nonequilibrium phase transitions. Characteristics of the behavior of the statistical system are obtained: an explicit form of the stationary distribution of the number of domains; ratios for the phase transition points; the expression for the first two moments of the random domain concentration, and the expression for the lifetime of membrane domains in the stationary state.     

Experimental Study of Ant Movement in a Straight Passageway under Stress Conditions

In the present study, we investigated whether single-file traffic of the ant Camponotus japonicus would exhibit a transition to traffic-jamming with increasing density under stress conditions. Previous work indicated that this transition did not occur in non-stressed ants, in contrast to data from pedestrians and vehicular traffic. Citronella oil was used to elicit ant movement from one end of a unidirectional passage to the other. The movements were recorded with a video camera, and the speed and distance travelled were extracted using image processing. We provided fundamental diagrams of ant traffic for small and large ants under stress conditions. Examination of the relationship between flow rate and density revealed no evidence of jamming, different from pedestrian and vehicular traffic. Concerning the speed-density relationship, surprisingly, in contrast with human fundamental diagrams (vehicular and pedestrian), we found that speed seemed to be constant with density within the experimental error. This study provided novel experimental data on ant traffic and might inform future studies of collective behavior of social insects and traffic systems.     

Adsorption Behavior of Polydisperse Polymeric Systems

Adsorption behavior of polydisperse polymers at interfaces is studied by the Monte Carlo simulation method based on a lattice model. Effects of temperature and adsorption energies on the polymer density profile, cluster distributions and adsorption layer thickness are evaluated in two different polydisperse systems. It is found that adsorption properties are greatly different in these two systems. In normal distribution polydisperse systems, polymers are more sensitive to the excluded volume effects while in average distribution polymers are more inclined to adsorb on adsorbing interfaces. As higher temperature and lower attraction constrain the polymer adsorption, more clusters are found under these conditions. When temperature approaches the critical temperature of monodisperse systems, stable and large clusters exist in these two polydisperse systems. These results suggest that micro phase transition may exist in polydisperse systems. Polydisperse systems take little change of phase transition temperatures but altered the clusters morphology to some extent. The adsorption layer thickness changes are more sensitive to both temperature and polymer–interface interactions in average distribution systems when the whole polymer concentration increases slightly. This work also suggests significant differences between the polydisperse and the monodisperse systems in adsorption behavior. Therefore, quantitative system errors may exist when the monodisperse system models are used in simulation to evaluate polymer adsorption properties.     

Robust scaling in ecosystems and the meltdown of patch size distributions before extinction

Robust critical systems are characterized by power laws which occur over a broad range of conditions. Their robust behaviour has been explained by local interactions. While such systems could be widespread in nature, their properties are not well understood. Here, we study three robust critical ecosystem models and a null model that lacks spatial interactions. In all these models, individuals aggregate in patches whose size distributions follow power laws which melt down under increasing external stress. We propose that this power-law decay associated with the connectivity of the system can be used to evaluate the level of stress exerted on the ecosystem. We identify several indicators along the transition to extinction. These indicators give us a relative measure of the distance to extinction, and have therefore potential application to conservation biology, especially for ecosystems with self-organization and critical transitions.     

Traffic Noise and Inequality in the Twin Cities,Minnesota

It is widely known that prolonged exposure to high levels of traffic noise has several health effects. While scholarship in environmental justice has explored the environmental equity hypothesis in a wide range of areas, whether the spatial distribution of traffic noise is equitable among different racial and socioeconomic groups has rarely been explored, especially in the United States. This article addresses this lacuna by examining this relationship in the Twin Cities Metro Region, Minnesota. Traffic data from the Minnesota Department of Transportation were used to model the propagation of traffic noise over the study area and aircraft noise contour lines were added to account for aircraft noise. Inequities associated with exposure to chronic traffic noise were investigated using selected demographic and socioeconomic variables from the U.S. Census 2000. Statistical analysis was based on a regression model that addressed spatial autocorrelation. Results indicate that there is an association between noise levels and household income, median household value, the percentage of non-white residents, and the percentage of the population less than 18 years of age.     

The effect of bacteriorhodopsin, detergent and hydration on the cubic-to-lamellar phase transition in the monoolein-distearoyl phosphatidyl glycerol-water system

The cubic phase of monoolein (MO) has successfully been used for crystallization of membrane proteins. It is likely that the transition to a lamellar phase upon dehydration is important for the crystallization process, and that the internal dimensions of the lipid phases (i.e., water pore diameter) are crucial for the inclusion and the diffusion of membrane proteins. In the present study, we investigated the cubic-to-lamellar phase transitions in the MO-water and the MO-distearoyl phosphatidyl glycerol (DSPG) systems. The MO-water system was investigated by means of isothermal sorption and desorption microcalorimetry. We show that the transition from cubic to lamellar phase induced by desorption is driven by entropy. At 25 degrees C, this occurs at a water activity of 0.98 with a transition enthalpy of 860 J/mol (MO). The phase behavior was also investigated in the presence of a small amount of the transmembrane protein bacteriorhodopsin (bR), and a detergent, octyl glucoside (OG), and it was shown that both bR and OG stabilize the lamellar phase. Analogous results were obtained for the MO-DSPG-water system. The latter system resembles the MO-water system in that a cubic-to-lamellar phase transition is induced by dehydration, although the structural properties of these phases are slightly different. Finally, we demonstrate that bR can be crystallized from a cubic phase of MO-DSPG-buffer.     

The Dynamic Behavior Possibilities of Raft-Like Domains in Biological Membranes

A possible scenario of the behavior of a raft-like domain system oscillating near the phase transition point of the Verchulst transition type, when the form of the stationary distribution for the concentration of domains changes stepwise, has been considered. A stationary state of the system is also possible at the indicated phase transition point, as well as fluctuations in the state of the system between the modes of extinction and survival, if the analogy with the Verhulst model is applied. The system behavior is explored in the framework of the stochastic storage model. This model is compared with the Verhulst model of a biological population. Similarities and differences between the models are highlighted. There are no bifurcations and transition to chaos in the domain system. Other features and characteristics of the dynamic behavior and stationary states of the raft-like domain system are considered.     

Collision avoidance in commercial aircraft Free Flight via neural networks and non-linear programming

In recent years there has been a great effort to convert the existing Air Traffic Control system into a novel system known as Free Flight. Free Flight is based on the concept that increasing international airspace capacity will grant more freedom to individual pilots during the enroute flight phase, thereby giving them the opportunity to alter flight paths in real time. Under the current system, pilots must request, then receive permission from air traffic controllers to alter flight paths. Understandably the new system allows pilots to gain the upper hand in air traffic. At the same time, however, this freedom increase pilot responsibility. Pilots face a new challenge in avoiding the traffic shares congested air space. In order to ensure safety, an accurate system, able to predict and prevent conflict among aircraft is essential. There are certain flight maneuvers that exist in order to prevent flight disturbances or collision and these are graded in the following categories: vertical, lateral and airspeed. This work focuses on airspeed maneuvers and tries to introduce a new idea for the control of Free Flight, in three dimensions, using neural networks trained with examples prepared through non-linear programming.     

溶剂特性对三臂星型类弹性蛋白多肽相变温度的影响

本文利用SpyTag/SpyCatcher特性构建了三臂星型结构的类弹性蛋白多肽(elastin like polypeptides, ELPs),考察其在不同溶剂,如分子拥挤试剂、osmolytes及深共熔溶剂(deep eutectic solvents,DESs)中的相变温度及行为,并与含有相同ELPs重复数的线性ELPs120作对比。结果表明：在不同浓度拥挤试剂PEG2000作用下,两种结构的ELPs相变温度均降低,当其各自浓度均为25 μmol/L时,三臂星型ELPs相变温度降低3℃～13℃,而ELPs120相变温度仅降低1.5℃～10.8℃。此外,在添加PEG2000后,三臂星型ELPs相变缓慢;在不同类型和浓度的osmolytes溶液中,25 μmol/L三臂星型ELPs相变温度明显要比线性ELPs高8℃左右;在DESs体系中,三臂星型ELPs有类似与水溶液中的相变行为,且其相变温度受到抑制,另外三臂星型ELPs和ELPs120在DESs/PBS体系中,与在(氯化胆碱+尿素)/PBS体系中的相变行为一致,其中当DESs体积含量为50%,ELPs120相变温度是最低的。由于ELPs在非单一缓冲液体系中的相变行为不同,这丰富了ELPs作为纯化标签的应用,且在非单一缓冲液体系中因降低了相变温度,节约了纯化融合蛋白的经济成本,同时也为研究ELPs拓扑结构与其相变行为之间的关系奠定理论基础。     

Multimodal peptide ligand extracts parvovirus from interface in affinity aqueous two-phase system

Aqueous two-phase systems (ATPS) have found various applications in bioseparations and microencapsulation. The primary goal of this technique is to partition target biomolecules in a preferred phase, rich in one of the phase-forming components. However, there is a lack of understanding of biomolecule behavior at the interface between the two phases. Biomolecule partitioning behavior is studied using tie-lines (TL), where each TL is a group of systems at thermodynamic equilibrium. Across a TL, a system can either have a bulk PEG-rich phase with citrate-rich droplets, or the opposite can occur. We found that porcine parvovirus (PPV) was recovered at a higher amount when PEG was the bulk phase and citrate was in droplets and that the salt and PEG concentrations are high. To improve the recovery, A PEG 10 kDa-peptide conjugate was formed using the multimodal WRW ligand. When WRW was present, less PPV was caught at the interface of the two-phase system, and more was recovered in the PEG-rich phase. While WRW did not significantly increase the PPV recovery in the high TL system, which was found earlier to be optimal for PPV recovery, the peptide did greatly enhance recovery at a lower TL. This lower TL has a lower viscosity and overall system PEG and citrate concentration. The results provide both a method to increase virus recovery in a lower viscosity system, as well as provide interesting thoughts into the interfacial phenomenon and how to recover virus in a phase and not at the interface.