bluuebunny/crossref_metadata_2025 huggingface dataset:
A simulation model of the bus transitway (TRNSIM)
Authors: Zargari Shahriar A. , Khan Ata M.
Published: January 2010

For planning and design of a bus rapid transit system and for the analysis of multimodal corridors, methodology is required for simulating bus traffic operation on a Transitway. Macroscopic models of vehicle flow are gaining popularity due to their capability to analyze complex operations and yet offer efficiency in development and applications. A macroscopic model is developed for the investigation of travel time, energy and emissions that correspond to bus volume levels on the Transitway. This paper describes the travel time part of the model. The model treats stochastic characteristics of bus traffic and passenger activities. Also, safety regimes in vehicle flow and factors affecting minimum headways in station areas are incorporated. The model is verified by comparing simulated travel time for the Ottawa‐Carleton Transitway with actual data.
An automatic segmentation procedure for studying variations in mode choice behaviour
Authors: Badoe Daniel A. , Miller Eric J.
Published: January 2010

Urban areas are very complex and heterogeneous in terms of their population composition and activity systems. The transport system, modal choices and service levels available to the population also varies considerably across space and time. These similarities and differences in choices and levels of explanatory variables facing individual tripmakers have to be explicitly considered in any study of transport behvior. The common practice has been to include user attributes, in addition to the system characteristics, in the modal utility functions to help capture differences in choice behavior across individuals. However, it could well be that the mode‐choice behavior of a segment of the population is fundamentally different from other segments of the population. In view of this, some studies have applied segmentation schemes to help identify the subgroups of presumably different travel responses. Typically, such schemes have been based on stratification of the population by a single variable, chosen either based on a priori notions or one‐way cross tabulations. These have their shortcomings. Thus, this paper develops an analytical procedure that simultaneously deals with level of service, socioeconomic and spatial factors to determine the relative role each plays in determining travel behavior. The procedure is applied to data from the Toronto region to illustrate its use.
Establishing a basic guideline for the selection of hov alternatives: The taiwan approach
Authors: Chang Tang‐Hsien , Chiu Hsien‐Ming
Published: January 2010

This paper presents a method for applying HOV lanes to the Taiwan freeway system. The purpose is to develop guidelines for designating alternative HOV lanes on existing freeways. Simulation results suggest that introducing HOV facilities would significantly improve traffic delays for short and long term steady states, especially during peak hour traffic flow. To ensure the success of the proposed HOV facilities, special attention should be devoted to public awareness and communication, as well as to related planning, education and enforcement issues.
Hybrid model of taxonomy and genetic algorithms for finding shortest path in transportation systems
Authors: Soehodho Sutanto
Published: January 2010

This is research is aimed at elaborating a new methodology of shortest path finding by utilizing the methods of taxonomy and genetic algorithms. Combination of the two is developed and called Genetic Taxonomy Evaluator (GTE) which is expected to be an alternative tool to solve shortest path finding problems within the transportation networks While keeping the properties of transportation networks Taxonomy Reconstructor (TR) transforms the network representation into taxonomic structure, which is hierarchically shaped, based on problem to be solved. In the process TR also creates classification of nodes in the network. This classification provides facilities to isolate the problem to the core, and the criteria that can be inserted in the Genetic Algorithm (GA). A package program for GTE is then developed in C‐Language and performance of model is analyzed upon a medium scale of Sioux‐Falls City Network. In conclusion, it is found that to achieve fairly quick convergence of GTE computation several optimal parameters of GA should be determined prior to searching for the shortest paths. And since GTE has only been applied to limited case, it is suggested that the findings could be a threshold for further researches.
The supply side of the automated people mover market: A spectrum of choices
Authors: Didrikson Paul V. , Nickerson Kathryn
Published: January 2010

A survey of the supply side of the Automated People Mover (APM) market over the past ten to fifteen years shows some significant trends. In the nineteen eighties, suppliers concentrated on designing, developing, and marketing unique technologies. Thus, each supplier tended to specialize in a single technology, with some variations in size and capacity. With the present growth of the APM market, several APM suppliers have developed, either through mergers or acquisitions, a more diversified range of technologies to meet a variety of system requirements in terms of capacity, service and budget considerations. As a result of this trend, the transit industry now has a full range of technologies that are well proven and capable of meeting the different needs, special operational requirements, and budgets of its potential clients.
Evaluation of network reliability using stochastic user equilibrium
Authors: Asakura Yasuo
Published: January 2010

When we evaluate the performance reliability of a network, it is necessary to describe user's behaviour in a partially degraded network. This paper shows that the Stochastic User Equilibrium (SUE) model assuming user's route choice behaviour under uncertain network conditions can be incorporated in the performance reliability model. The effects of providing information are analyzed using the SUE model with two different groups of route choice; informed drivers and non informed drivers. It is found that providing information generally increases network performance reliability. This depends, however, on the probability distribution of the network states.
A traffic flow simulator for network reliability assessment
Authors: Lam William H. K. , Xu G.
Published: January 2010

This paper investigates the transportation network reliability based on the information provided by detectors installed on some links. A traffic flow simulator (TFS) model is formulated for assessing the network reliability (in terms of travel time reliability), in which the variation of perceived travel time error and the fluctuations of origin‐destination (OD) demand are explicitly considered. On the basis of prior OD demand and partial updated detector data, the TFS can estimate the link flows for the whole network together with link/path travel times, and their variance and covariance. The travel time reliability by OD pair can also be assessed and the OD matrix can be updated simultaneously. A Monte Carlo based algorithm is developed to solve the TFS model. The application of the proposed TFS model is illustrated by a numerical example.
A review of the state of the art of personal rapid transit
Authors: Anderson J. Edward
Published: January 2010

The paper begins with a review of the rational for development of personal rapid transit, the reasons it has taken so long to develop, and the process needed to develop it. Next I show how the PRT concept can be derived from a system‐significant equation for life‐cycle cost per passenger‐mile as the system that minimizes this quantity. In the bulk of the paper I discuss the state‐of‐the‐art of a series of technical issues that had to be resolved during the development of an optimum PRT design. These include capacity, switching, the issue of hanging vs. supported vehicles, guideways, vehicles, control, station operations, system operations, reliability, availability, dependability, safety, the calculation of curved guideways, operational simulation, power and energy. The paper concludes with a listing of the implications for a city that deploys an optimized PRT system.
Greenhouse gas reduction potential of advanced traffic control
Authors: Alkadry Abdulkader , Khan Ata M.
Published: January 2010

Reducing greenhouse gas (GHG) emissions from transportation in the context of the climate change issue and the associated Kyoto Agreement of 1997 is a challenge. Since urban transportation is a major contributor to greenhouse gases, measures are required to reduce these emissions. Given that during peak periods, road vehicles propelled by petroleum fuel‐based internal combustion engines produce a high level of GHG emissions due to stop and go operations, measures to improve traffic flow can play an effective mitigation role. This paper describes a simulation‐based methodology and a case study for the quantification of GHG emission reduction owing to advanced traffic control systems.
The planning of aircraft routes and flight frequencies in an airline network operations
Authors: Yan Shangyao , Wang Chung‐Rey
Published: January 2010

This research is aimed at developing a model that maximizes system profit when determining the aircraft routes and flight frequencies in a network. The model employs network flow techniques to effectively collect or deliver passenger flows from all origins to all destinations using non‐stop and multi‐stop flights in multi‐fleet operations. The model was formulated as a multi‐commodity network flow problem. A Lagrangian‐based algorithm was developed to solve the problem. To test the model in practice, a case study is presented.
Characterization of incidents on an urban arterial road
Authors: Luk James Y. K. , Chung Edward C. S. , Sin Francis Y. C.
Published: January 2010

The early warning of incidents on urban arterial roads in a congested city can reduce delay, accidents and pollutant emission. Freeway incident detection systems implemented in recent years may not be suitable for arterial incidents. Arterial incident detection is more difficult. The traffic flow on an arterial road is not conserved from the upstream end of a road link to the downstream end because urban traffic does turn in and out of side‐streets, car‐parks and local residences. Roadside friction such as kerbside parking and shopping traffic also tends to create apparent incidents which are in fact frequent and normal events. This paper develops a definition for an arterial incident and describes a case study on an arterial road in Melbourne, Australia. The study shows that detectors upstream of an incident are more useful for incident detection than downstream detectors. It also identifies occupancy and speed as the appropriate parameters to characterise and detect arterial incidents.
A schedule‐based dynamic transit network model — Recent advances and prospective future research
Authors: Tong C. O. , Wong S. C. , Poon M. H. , Tan M. C.
Published: January 2010

Using the schedule‐based approach, in which scheduled timetables are used to describe the movement of vehicles, a dynamic transit assignment model is formulated. Passengers are assumed to travel on a path with minimum generalized cost that consists of four components: in‐vehicle time; waiting time; walking time; and a time penalty for each line change. A specially developed branch and bound algorithm is used to generate the time‐dependent minimum path. The assignment procedure is conducted over a period in which both passenger demand and train headway are varying. This paper presents an overview of the research that has been carried out by the authors to develop the schedule‐based transit assignment model, and offers perspectives for future research.
Fare deregulation of transit services: Winners and losers in a competitive market
Authors: Lo Hong K. , Yip C. W.
Published: January 2010

Currently, the Hong Kong government imposes fare control on buses and taxi while the rail services are immune to such a control. This study examined four scenarios of fare deregulation on transit services by considering three related parties of a transit system – service providers, travelers, and society in general, with their respective objectives represented as – revenue, travel utility, and congestion. Analyzing the resultant impacts on these three parties, we found that a different regulatory environment would favor or hurt a different set of parties. There is no clear win‐win situation for all parties. Deciding a socially acceptable regulatory environment is likely to involve difficult tradeoffs among these parties.
Behavioral monitoring of public transport users through a mobile communication system
Authors: Asakura Yasuo , Hato Eiji
Published: January 2010

There are various activities now taking place in ITS research and development in Japan. Advanced information and communication technologies have been applied to improve public transport systems, as well as automated highway systems. In the first part of this paper, we show three examples of public transport systems recently developed in ITS environment. These transport systems are operated in local cities and towns in Japan: the travel information system for tram users in Hiroshima, the demand responsive bus system in Nakamura and the co‐operative use of electric vehicle in Ebina. In the second part of the paper, we explain how we have monitored individual passenger on public transport using cellular phones for location positioning. Location positioning technology for mobile object is essential for the operation and management of ITS supported public transport systems. Furthermore, such accurate and detailed positioning data can be utilized for travel behaviour analysis in demand modeling. The mobile instrument and monitoring systems shown in this paper can be combined with any of the case studies of ITS application to public transport systems.
Optimization of grid bus transit systems with elastic demand
Authors: Chien Steven I‐Jy , Spasovic Lazar N.
Published: January 2010

Current analytic models for optimizing urban bus transit systems tend to sacrifice geographic realism and detail in order to obtain their solutions. The models presented here shows how an optimization approach can be successful without oversimplifying spatial characteristics and demand patterns of urban areas and how a grid bus transit system in a heterogeneous urban environment with elastic demand is optimized. The demand distribution over the service region is discrete, which can realistically represent geographic variation. Optimal network characteristics (route and station spacings), operating headways and fare are found, which maximize the total operator profit and social welfare. Irregular service regions, many‐to‐many demand patterns, and vehicle capacity constraints are considered in a sequential optimization process. The numerical results show that at the optima the operator profit and social welfare functions are rather flat with respect to route spacing and headway, thus facilitating the tailoring of design variables to the actual street network and particular operating schedule without a substantial decrease in profit. The sensitivities of the design variables to some important exogenous factors are also presented.
Express guideway transit: A case for further development in transit automation
Authors: Batelaan Justin
Published: January 2010

Safe and reliable coupling and decoupling of cars from a moving train is feasible with further developments in linear motor propulsion and control of transit vehicles. This allows the last car of a train to decouple and stop at a station for a relative long dwell time, before it accelerates and is coupled to a following train. Controlled doors in front and rear of the transit vehicle permit passengers to walk through the train to the car which stops at their destination. A proposed transit system using these features is described and compared to Bombardier's Advanced Rapid Transit. Potential advantages are high schedule speed, uncrowded trains, smaller and more stations, low energy requirements and a smaller vehicle fleet.
The future for in‐vehicle information systems: The technology and its impacts
Authors: Bell Michael G H
Published: January 2010

In‐vehicle information has an important social role to play in improving the efficiency and safety of travel by all modes. In this review, three generations of system are identified. The first generation consists of simple in‐vehicle units relying heavily on external data. The second generation has more sophisticated in‐vehicle units with colour TFT screens and DVD players for maps and entertainment. The third generation again makes use of external data, using the mobile phone network to download map sections and other data as and when required, thereby obviating the need for beacons and map CDs. For locationing, GPS (and/or Galileo, the European version of GPS) remains the favoured technology. Portable devices offering multi‐modal information could improve inter‐modal transport efficiency.
A traffic flow simulator for short‐term travel time forecasting
Authors: Lam William H. K. , Chan K. S. , Shi John W. Z.
Published: January 2010

This paper presents an off‐line forecasting system for short‐term travel time forecasting. These forecasts are based on the historical traffic count data provided by detectors installed on Annual Traffic Census (ATC) stations in Hong Kong. A traffic flow simulator (TFS) is developed for short‐term travel time forecasting (in terms of offline forecasting), in which the variation of perceived travel time error and the fluctuations of origin‐destination (O‐D) demand are considered explicitly. On the basis of prior O‐D demand and partial updated detector data, the TFS can estimate the link travel times and flows for the whole network together with their variances and covariances. The short‐term travel time forecasting by O‐D pair can also be assessed and the O‐D matrix can be updated simultaneously. The application of the proposed off‐line forecasting system is illustrated by a numerical example in Hong Kong.
Adaptive traffic control system: Control strategy, prediction, resolution, and accuracy
Authors: Lo Hong K. , Chow H. F.
Published: January 2010

Recent advances in traffic control methods have led to flexible control strategies for use in an adaptive traffic control system (ATCS). ATCS aims at controlling the imminent traffic, which is yet to arrive and hence not known perfectly. Therefore, volume prediction is an essential part. Associated with the prediction are two aspects: resolution and accuracy. Recent studies indicate a tradeoff between prediction resolution and accuracy: finer resolutions, larger errors. It is imperative to study the relationship and tradeoff between the control strategy, prediction resolution, and its associated error, which are crucial to the development of ATCS. This study investigates this relationship through an extensive simulation of scenarios in Hong Kong with a recently developed dynamic traffic control model, DISCO. Based on the Hong Kong scenarios conducted with DISCO, the major findings include: (i) the importance of resolution outweighs that of error; (ii) dynamic timing plans generally outperform time‐invariant timing plans; (iii) up to a certain extent, overestimated predictions lead to better results than underestimated predictions.
Automated transit headway control via adaptive signal priority
Authors: Ling Kenny , Shalaby Amer
Published: January 2010

This paper reports on a study that developed a next‐generation Transit Signal Priority (TSP) strategy, Adaptive TSP, that controls adaptively transit operations of high frequency routes using traffic signals, thus automating the operations control task and relieving transit agencies of this burden. The underlying algorithm is based on Reinforcement Learning (RL), an emerging Artificial Intelligence method. The developed RL agent is responsible for determining the best duration of each signal phase such that transit vehicles can recover to the scheduled headway taking into consideration practical phase length constraints.

A case study was carried out by employing the microscopic traffic simulation software Paramics to simulate transit and traffic operations at one signalized intersection along the King Streetcar route in downtown Toronto. The results show that the control policy learned by the agent could effectively reduce the transit headway deviation and causes smaller disruption to cross street traffic compared with the existing unconditional transit signal priority algorithm.
Real time traffic information and its impacts on route switching behavior of expressway drivers
Authors: Jou Rong‐Chang , Lam Soi‐Hoi , Weng Mei‐Chuan , Chen Chih‐Cheng
Published: January 2010

Non‐quantifiable factors (e.g. perceived, attitudinal and preferential factors) have not been investigated fully in past transportation studies, which has raised questions on the predictive capabilities of the models. In this study, Structure Integration Models, with one of their sub‐models, Measurement Equation, are combined with latent variables, which are integrated with another sub‐model, Structural Equation. The estimated latent variables are used as explanatory variables in decision models. As a result, the explanatory and predictive capabilities of the models are enhanced. The models can then be used to describe the various behaviors of travelers of different types of transportation systems in a more accurate way. In this study, the Structure Integration Model was applied to study the impacts of real‐time traffic information on the route‐switching behavior of road users on the Sun Yat‐Sen expressway, Taiwan. At present, the real‐time traffic information provided on this expressway includes radio traffic reports and changeable message signs. The results of this study can facilitate the provision of traffic information on highways.
Sensitivity analysis on stochastic equilibrium transportation networks using genetic algorithm
Authors: Ceylan Halim , Bell Michael G. H.
Published: January 2010

This study deals with the sensitivity analysis of an equilibrium transportation networks using genetic algorithm approach and uses the bi‐level iterative sensitivity algorithm. Therefore, integrated Genetic Algorithm‐TRANSYT and Path Flow Estimator (GATPFE) is developed for signalized road networks for various level of perceived travel time in order to test the sensitivity of perceived travel time error in an urban stochastic road networks. Level of information provided to drivers correspondingly affects the signal timing parameters and hence the Stochastic User Equilibrium (SUE) link flows. When the information on road system is increased, the road users try to avoid conflicting links. Therefore, the stochastic equilibrium assignment concept tends to be user equilibrium. The GATPFE is used to solve the bi‐level problem, where the Area Traffic Control (ATC) is the upper‐level and the SUE assignment is the lower‐level. The GATPFE is tested for six‐junction network taken from literature. The results show that the integrated GATPFE can be applied to carry out sensitivity analysis at the equilibrium network design problems for various level of information and it simultaneously optimize the signal timings (i.e. network common cycle time, signal stage and offsets between junctions).
The simple platoon advancement model of its technologies applied to vehicle control at signalised intersections
Authors: Clement Stuart , Taylor Michael
Published: January 2010

The Simple Platoon Advancement (SPA) Model describes a conceptual system whose principal objective is to increase the throughput of vehicles at signalised intersections. This is achieved through a novel combination of Intelligent Transport System (ITS) technologies including Automatic Cruise Control, Lane Departure Avoidance, and Collision Avoidance. These are combined in SPA so that vehicles are progressed through signalised intersections under automated control. All of the vehicles in a stationary queue are moved instantly at the start‐of‐green as a closely‐spaced platoon. Dispersion occurs after all vehicles are in motion. Throughput of the SPA model is determined analytically and comparisons are made between the SPA model and a valid representation of current road traffic behaviour. These comparisons show that theoretically a SPA system can progress nearly twice as many vehicles past the stopline as can be seen in today's road network. Other benefits of a conceptual SPA system are improved safety and a reduction in delay per vehicle.
The importance of information flows temporal attributes for the efficient scheduling of dynamic demand responsive transport services
Authors: Diana Marco
Published: January 2010

The operation of a demand responsive transport service usually involves the management of dynamic requests. The underlying algorithms are mainly adaptations of procedures carefully designed to solve static versions of the problem, in which all the requests are known in advance. However there is no guarantee that the effectiveness of an algorithm stays unchanged when it is manipulated to work in a dynamic environment. On the other hand, the way the input is revealed to the algorithm has a decisive role on the schedule quality. We analyze three characteristics of the information flow (percentage of real‐time requests, interval between call‐in and requested pickup time and length of the computational cycle time), assessing their influence on the effectiveness of the scheduling process.
Estimation of a time‐dependent origin‐destination matrix for congested highway networks
Authors: Cheung W. M. , Wong S. C. , Tong C. O.
Published: January 2010

This paper presents a time‐dependent origin‐destination (O‐D) matrix estimation procedure embedded with a dynamic traffic assignment model, in which the predictive dynamic user optimal conditions in congested networks are maintained. Two solution algorithms are proposed, namely: an iterative (ITR) scheme and a method of successive averages (MSA) scheme. It is found that the MSA scheme outperforms the ITR scheme. As a prior O‐D matrix is an important input for the problem, its quality is essential for the reliability of the matrix estimation procedure. Empirical constraints are set in relation to the quality of the prior O‐D matrix for the estimation procedure. Numerical examples are used to demonstrate the effectiveness of the proposed methodology.
Homocysteine metabolism and its relation to health and disease
Authors: Williams Kelly T. , Schalinske Kevin L.
Published: January 2010

Homocysteine is a metabolic intermediate in methyl group metabolism that is dependent on a number of nutritional B‐vitamin cofactors. An emerging aspect of homocysteine metabolism is its relation to health and disease. Perturbations of homocysteine metabolism, particularly intracellular and subsequently circulating accumulation of homocysteine (i.e., hyperhomocysteinemia), are associated with vascular disease risk, as well as other pathologies. However, intervention with B‐vitamin supplementation has been shown to successfully restore normal homocysteine concentrations, but without concomitant reductions in disease risk. Thus, the mechanistic relation between homocysteine balance and disease states, as well as the value of homocysteine management, remains an area of intense investigation.
Fibrillar peptide gels in biotechnology and biomedicine
Authors: Jung Jangwook P. , Gasiorowski Joshua Z. , Collier Joel H.
Published: January 2010

Peptides, peptidomimetics, and peptide derivatives that self‐assemble into fibrillar gels have received increasing interest as synthetic extracellular matrices for applications in 3D cell culture and regenerative medicine. Recently, several of these fibrillizing molecules have been functionalized with bioactive components and chemical features such as cell‐binding ligands, degradable sequences, drug eluting compounds, and cross‐linkable groups, thereby producing gels that can reliably display multiple factors simultaneously. This capacity for incorporating precise levels of many different biological and chemical factors is advantageous given the natural complexity of cell–matrix interactions that many current biomaterial strategies seek to mimic. In this review, recent efforts in the area of fibril‐forming peptide materials are described, and advantages of biomaterials containing multiple modular elements are outlined. In addition, a few hurdles and open questions surrounding fibrillar peptide gels are discussed, including issues of the materials' structural heterogeneity, challenges in fully characterizing the diversity of their self‐assembled structures, and incomplete knowledge of how the materials are processed in vivo. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94: 49–59, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Self‐assembly of peptide amphiphiles: From molecules to nanostructures to biomaterials
Authors: Cui Honggang , Webber Matthew J. , Stupp Samuel I.
Published: January 2010

Peptide amphiphiles are a class of molecules that combine the structural features of amphiphilic surfactants with the functions of bioactive peptides and are known to assemble into a variety of nanostructures. A specific type of peptide amphiphiles are known to self‐assemble into one‐dimensional nanostructures under physiological conditions, predominantly nanofibers with a cylindrical geometry. The resultant nanostructures could be highly bioactive and are of great interest in many biomedical applications, including tissue engineering, regenerative medicine, and drug delivery. In this context, we highlight our strategies for using molecular self‐assembly as a toolbox to produce peptide amphiphile nanostructures and materials and efforts to translate this technology into applications as therapeutics. We also review our recent progress in using these materials for treating spinal cord injury, inducing angiogenesis, and for hard tissue regeneration and replacement. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:1–18, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Protein‐ and peptide‐modified synthetic polymeric biomaterials
Authors: Krishna Ohm D. , Kiick Kristi L.
Published: January 2010

This review presents an overview on bio‐hybrid approaches of integrating the structural and functional features of proteins and peptides with synthetic polymers and the resulting unique properties in such hybrids, with a focus on bioresponsive/bioactive systems with biomaterials applications. The review is divided in two broad sections. First, we describe several examples of bio‐hybrids produced by combining versatile synthetic polymers with proteins/enzymes and drugs that have resulted in (1) hybrid materials based on responsive polymers, (2) responsive hydrogels based on enzyme‐catalyzed reactions, protein–protein interactions and protein–drug sensing, and (3) dynamic hydrogels based on conformational changes of a protein. Next, we present hybrids produced by combining synthetic polymers with peptides, classified based on the properties of the peptide domain: (1) peptides with different conformations, such as α‐helical, coiled‐coil, and β‐sheet; (2) peptides derived from structural protein domains such as silk, elastin, titin, and collagen; and (3) peptides with other biofunctional properties such as cell‐binding domains and enzyme‐recognized degradation domains. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:32–48, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Polysaccharide‐modified synthetic polymeric biomaterials
Authors: Baldwin Aaron D. , Kiick Kristi L.
Published: January 2010

This review presents an overview of polysaccharide‐conjugated synthetic polymers and their use in tissue‐engineered scaffolds and drug‐delivery applications. This topic will be divided into four categories: (1) polymeric materials modified with non‐mammalian polysaccharides such as alginate, chitin, and dextran; (2) polymers modified with mammalian polysaccharides such as hyaluronan, chondroitin sulfate, and heparin; (3) multi‐polysaccharide‐derivatized polymer conjugate systems; and (4) polymers containing polysaccharide‐mimetic molecules. Each section will discuss relevant conjugation techniques, analysis, and the impact of these materials as micelles, particles, or hydrogels used in in‐vitro and in‐vivo biomaterial applications. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:128–140, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Molecular biomimetics: GEPI‐based biological routes to technology
Authors: Tamerler Candan , Khatayevich Dmitriy , Gungormus Mustafa , Kacar Turgay , Oren E. Emre , Hnilova Marketa , Sarikaya Mehmet
Published: January 2010

In nature, the viability of biological systems is sustained via specific interactions among the tens of thousands of proteins, the major building blocks of organisms from the simplest single‐celled to the most complex multicellular species. Biomolecule‐material interaction is accomplished with molecular specificity and efficiency leading to the formation of controlled structures and functions at all scales of dimensional hierarchy. Through evolution, Mother Nature developed molecular recognition by successive cycles of mutation and selection. Molecular specificity of probe‐target interactions, e.g., ligand‐receptor, antigen–antibody, is always based on specific peptide molecular recognition. Using biology as a guide, we can now understand, engineer, and control peptide‐material interactions and exploit them as a new design tool for novel materials and systems. We adapted the protocols of combinatorially designed peptide libraries, via both cell surface or phage display methods; using these we select short peptides with specificity to a variety of practical materials. These genetically engineered peptides for inorganics (GEPI) are then studied experimentally to establish their binding kinetics and surface stability. The bound peptide structure and conformations are interrogated both experimentally and via modeling, and self‐assembly characteristics are tested via atomic force microscopy. We further engineer the peptide binding and assembly characteristics using a computational biomimetics approach where bioinformatics based peptide‐sequence similarity analysis is developed to design higher generation function‐specific peptides. The molecular biomimetic approach opens up new avenues for the design and utilization of multifunctional molecular systems in a wide‐range of applications from tissue engineering, disease diagnostics, and therapeutics to various areas of nanotechnology where integration is required among inorganic, organic and biological materials. Here, we describe lessons from biology with examples of protein‐mediated functional biological materials, explain how novel peptides can be designed with specific affinity to inorganic solids using evolutionary engineering approaches, give examples of their potential utilizations in technology and medicine, and, finally, provide a summary of challenges and future prospects. © 2010 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 94:78–94, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Potential allosteric modulators of the proteasome activity
Authors: Jankowska E. , Gaczynska M. , Osmulski P. , Sikorska E. , Rostankowski R. , Madabhushi S. , Tokmina‐Lukaszewska M. , Kasprzykowski F.
Published: January 2010

Proteasome, consisting of a tube‐shaped proteolytic core particle and attached to it regulatory modules, is a multifunctional enzymatic complex essential for the ubiquitin‐proteasome metabolic pathway. Due to its immense involvement in regulation of cellular physiology, the proteasome is an acknowledged anticancer drug target and potential target to treat inflammatory or degenerative diseases. So far, competitive inhibitors of the core particle gain most consideration as drugs. We postulate that noncompetitively‐acting small‐molecule compounds would provide excellent means to precisely regulate actions of the proteasome. In this study, we evaluated five short peptides based on sequences of two proteins known to interact with the core proteasome: HIV‐1 Tat and PA28/REG activator. We performed Circular Dichroism (CD), Fourier Transformed Infrared Spectroscopy (FTIR), and Nuclear Magnetic Resonance (NMR) analysis, supplemented by MD simulations, and tested influence of the peptides on performance of the core particle active sites and functioning of regulatory modules. We found that PP2‐containing Tat peptides are noncompetitive inhibitors of the core, interfering with the actions of PA28αβ activator. In addition, at low concentrations the turn‐prone Tat2 is able to activate the latent core. The random coil‐structured PA28‐derived peptides display only weak or nondetectable direct effects on the core activities, exhibiting, however, a positive cooperation with activity‐enhancing actions of PA28αβ. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 481–495, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Vibrational spectroscopic studies of newly developed synthetic biopolymers
Authors: Bista Rajan K. , Bruch Reinhard F. , Covington Aaron M.
Published: January 2010

Vibrational spectroscopic techniques such as near‐infrared (NIR), Fourier transform infrared (FTIR), and Raman spectroscopy are valuable diagnostic tools that can be used to elucidate comprehensive structural information of numerous biological samples. In this review article, we have highlighted the advantages of nanotechnology and biophotonics in conjunction with vibrational spectroscopic techniques in order to understand the various aspects of new kind of synthetic biopolymers termed as polyethylene glycol (PEG)ylated lipids. In contrast to conventional phospholipids, these novel lipids spontaneously form liposomes or nanovesicles upon hydration, without the supply of external activation energy. The amphiphiles considered in this study differ in their hydrophobic acyl chain length and contain different units of PEG hydrophilic headgroups. We have further explored the thermotropic phase behaviors and associated changes in the conformational order/disorder of such lipids by using variable‐temperature FTIR and Raman spectroscopy. Phase transition temperature profiles and correlation between various spectral indicators have been identified by either monitoring the shifts in the vibrational peak positions or plotting vibrational peak intensity ratios in the CH stretching region as a function of temperature. To supplement our observations of phase transformations, a thermodynamic approach known as differential scanning calorimetry (DSC) has been applied and revealed a good agreement with the infrared and Raman spectroscopic data. Finally, the investigation of thermal properties of lipids is extremely crucial for numerous purposes, thus the results obtained in this work may find application in a wide variety of studies including the development of PEGylated lipid based drug and substances delivery vehicles. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 403–417, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Model peptide‐based system used for the investigation of metal ions binding to histidine‐containing polypeptides
Authors: Murariu Manuela , Dragan Ecaterina Stela , Drochioiu Gabi
Published: January 2010

The reaction of histidine‐containing polypeptides with toxic and essential metals and the molecular mechanism of complexation has yet to be determined, particularly with respect to the conformational changes of the interacting macromolecules. Therefore, a system of oligopeptides containing histidine residues in various positions of Ala or Gly sequences has been designed and used in heavy metal comparatively binding experiments. The role of spacing residues (Gly and Ala repeats) in selecting the various conformations was investigated. The newly synthesized peptides and metal ion adducts have been characterized by Fourier transform infrared spectroscopy (FTIR) as well as electrospray ion trap mass spectrometry (ESI–MS) and circular dichroism (CD). The analysis of CD‐spectra of the four peptides in water revealed that the secondary structure depends much on the position of each amino acid in the peptide backbone. Our peptides system reveals various binding mechanisms of metal ions to peptides depending on the position of histidine residue and the corresponding conformations of Ala or Gly sequences. Biological and medical consequences of conformational changes of metal‐bound peptides are further discussed. Thus, the binding of heavy metals to four peptides may serve as a model system with respect to the conformational consequences of the metal addition on the amino acid repeats situated in prion protein. © 2010 Wiley Periodicals, Inc. Biopolymers 93:497–508, 2010.

This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com
Photoregulated assembly/disassembly of DNA‐templated protein arrays using modified oligonucleotide carrying azobenzene side chains
Authors: Hachikubo You , Iwai Sosuke , Uyeda Taro Q.P.
Published: January 2010

DNA‐templated self‐assembly of nanomaterials provides great potential for applications including biosensors, nanoelectronics, and programmable and autonomous molecular machines. To switch or regulate the activities of those nanobiotechnological devices, non‐invasive methods to assemble and disassemble specific nanoscale components are needed. Here, we describe photocontrol of assembly of DNA‐templated protein arrays in solution, by using photo‐controlled duplex formation of oligonucleotides carrying azobenzene. As a proof of concept prototype, we designed a one‐dimensional protein array system that consists of a scaffold of DNA and two kinds of anchor DNA that were conjugated with fluorescent proteins (CFP and YFP, respectively). The scaffold DNA was modified to carry multiple azobenzene side chains so that the hybridization involving the scaffold DNA is regulated by photoirradiation through conformational changes of the azobenzene moieties. Melting temperatures of duplex made of the modified DNA scaffold and an anchor oligonucleotide were shifted significantly and reversibly by UV and visible photoirradiation (difference of Tm was 34.8°C in 150 mM potassium acetate). Measurements of Förster resonance energy transfer between CFP and YFP showed that the assembly of the protein array system was also changed by photoirradiation. Such non‐invasive and reversible method to control assembly/disassembly of multiple, specific proteins in a DNA‐templated protein array system would provide many functions for nanobiotechnological devices such as on/off switches and the ability to change the configuration reversibly. Biotechnol. Bioeng. 2010; 106: 1–8. © 2010 Wiley Periodicals, Inc.
Inhibitors of the Pseudomonas aeruginosa quorum‐sensing regulator, QscR
Authors: Liu Hai‐Bo , Lee Joon‐Hee , Kim Jung Sun , Park Sunghoon
Published: January 2010

QscR is a quorum‐sensing (QS) signal receptor that controls expression of virulence genes in the prevalent opportunistic pathogen, Pseudomonas aeruginosa. Unlike the previously reported LuxR‐type QS receptor proteins, that is, LasR and TraR, QscR can be obtained as an apo‐protein that can reversibly form an active complex in vitro with its cognate signal molecule, 3‐oxododecanoyl‐homoserine lactone (3OC12‐HSL), and subsequently bind to target promoter DNA sequences. To search for potential QS inhibitors, an in vitro gel retardation assay was developed using the purified QscR. Both the in vitro assay and the in vivo cell‐based assay using QscR‐overproducing recombinant strains were applied in the screening process. Furanones were chosen for testing the activity as QS inhibitors because they have been reported to strongly inhibit expression of QS‐related genes in Agrobacterium tumefaciens. Among more than a hundred furanones tested, three compounds showed strong and dose‐dependent inhibitory effects on QscR in both assays. One compound in particular, designated as F2, could completely inhibit the 3OC12‐HSL‐dependent QscR activity in vitro at a concentration of 50‐fold molar excess over 3OC12‐HSL. However, with the furanones F3 and F4, which are structurally similar to F2 but with a nitro group instead of the amine moiety, significantly decreased activities were observed. These results suggest that (i) the in vitro assay is a sensitive and reliable tool for screening QS inhibitors, and (ii) furanones are potentially important QS inhibitors for many LuxR‐type receptor proteins. Biotechnol. Bioeng. 2010; 106: 119–126. © 2010 Wiley Periodicals, Inc.
Anaerobic mixed‐culture fermentation of aqueous ammonia‐treated sugarcane bagasse in consolidated bioprocessing
Authors: Fu Zhihong , Holtzapple Mark T.
Published: January 2010

The MixAlco process is an example of consolidated bioprocessing (CBP) in which anaerobic mixed‐culture fermentation biochemically converts any biodegradable feedstock into carboxylate salts. Downstream processing thermochemically transforms the resulting salts into mixed alcohol fuels or gasoline. To enhance digestibility, sugarcane bagasse was treated under mild conditions (55°C, 24 h, and 30% aqueous ammonia solution with a loading of 10 mL/g dry biomass). Using NH4HCO3 buffer, the feedstock (80% ammonia‐treated sugarcane bagasse/20% chicken manure) was anaerobically fermented by a mixed culture of marine microorganisms at 55°C. Four‐stage countercurrent fermentations were performed at various volatile solids loading rates (VSLRs) and liquid residence times (LRTs). The highest acid productivity (1.14 g/(L day)) occurred at a total acid concentration of 29.8 g/L. The highest conversion (65%) occurred at a total acid concentration of 27.6 g/L. The continuum particle distribution model (CPDM) predicted the experimental total acid concentrations and conversions within 4.98% and 10.41%, respectively. When using NH4HCO3 buffer, ammonia pretreatment is an attractive option. The CPDM “map” shows that both high volatile solid conversions (78.8%) and high acid concentrations (32.6 g/L) are possible with 300 g/(L liquid) substrate concentration, 30 days LRT, 2 g/(L day) solid loading rate and NH4HCO3 buffer. Biotechnol. Bioeng. 2010;106: 216–227. © 2010 Wiley Periodicals, Inc.