Mechanisms of kinetic trapping in self-assembly and phase transformation

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions

Enhancing the CS Curriculum with with Aspect-Oriented Software Development (AOSD) and Early Experience

Aspect-oriented software development (AOSD) is evolving as an important step beyond existing software development approaches such as object-oriented development. An aspect is a module that captures a crosscutting concern, behavior that cuts across different units of abstraction in a software application; expressed as a module, such behavior can be enabled and disabled transparently and non-invasively, without changing the application code itself. Increasing industry demand for expertise in AOSD gives rise to the pedagogical challenge of covering this methodology and its foundations in the computer science curriculum. We present our curricular initiative to incorporate a novel course in AOSD in the undergraduate computer science curriculum at the intermediate level. We also discuss recent and planned efforts to integrate coverage of AOSD into existing courses

Understanding the Concentration Dependence of Viral Capsid Assembly Kinetics - the Origin of the Lag Time and Identifying the Critical Nucleus Size

The kinetics for the assembly of viral proteins into a population of capsids can be measured in vitro with size exclusion chromatography or dynamic light scattering, but extracting mechanistic information from these studies is challenging. For example, it is not straightforward to determine the critical nucleus size or the elongation time (the time required for a nucleated partial capsid to grow completion). We show that, for two theoretical models of capsid assembly, the critical nucleus size can be determined from the concentration dependence of the assembly reaction half-life and the elongation time is revealed by the length of the lag phase. Furthermore, we find that the system becomes kinetically trapped when nucleation becomes fast compared to elongation. Implications of this constraint for determining elongation mechanisms from experimental assembly data are discussed.Comment: Submitted to Biophysical Journa

Domain-Specific Multi-Modeling of Security Concerns in Service-Oriented Architectures

As a common reference for many in-development standards and execution frameworks, special attention is being paid to Service-Oriented Architectures. SOAs modeling, however, is an area in which a consensus has not being achieved. Currently, standardization organizations are defining proposals to offer a solution to this problem. Nevertheless, until very recently, non-functional aspects of services have not been considered for standardization processes. In particular, there exists a lack of a design solution that permits an independent development of the functional and non-functional concerns of SOAs, allowing that each concern be addressed in a convenient manner in early stages of the development, in a way that could guarantee the quality of this type of systems. This paper, leveraging on previous work, presents an approach to integrate security-related non-functional aspects (such as confidentiality, integrity, and access control) in the development of services

Periodic Route Optimization for Handed-off Connections in Wireless ATM Networks

In Wireless ATM networks, user connections need to be rerouted during handoff as mobile users move among base stations. The rerouting of connections must be done quickly with minimal disruption to traffic. In addition, the resulting routes must be optimal. A reasonable approach is to implement handoff in two phases. In the first phase connections are rapidly rerouted and in the second phase a periodic route optimization procedure is executed. The route optimization should impose minimal signaling and processing load on the ATM switches. In this paper, we propose and study a periodic execution of route optimization for a two-phase handoff scheme. We study two types of execution: non-adaptive and adaptive. For the adaptive optimization, we consider two adaptation schemes that are dependent on network conditions. A simulation model is developed to study system performance. The adaptive route optimization is shown to minimize signaling and processing load while maximizing utilization of reserved resources

Performance Study of a Two-Phase Handoff Scheme for Wireless ATM Networks

This paper presents an analytical and simulation study of a two-phase handoff scheme for rerouting user connection in Wireless ATM networks. The two-phase handoff scheme provides a rapid rerouting of user connections in the first phase utilizing permanent virtual paths reserved between adjacent Mobility Enhanced Switches (MES). In the second phase, a non-realtime route optimization procedure is executed to optimally reroute handed-off connection. In this paper, we study the performance of such a scheme as a function of various system load parameters. These parameters include originating call arrival rate, call holding time, and radio cell residual time. We examine the relation between the required bandwidth resources and optimization rate. Also we calculate and study the handoff blocking probability due to lack of bandwidth for resources reserved to facilitate the rapid rerouting

A Novel Handoff Scheme for Wireless ATM Networks

Mobility support and management in Wireless ATM networks poses a number of technical issues. An important issue is the ability to manage and reroute active connections during handoff as mobile users move among base stations. We propose a novel two-phase handoff scheme using permanent virtual paths reserved between adjacent Mobility Enhanced Switches (MES). The virtual paths are used in the first phase to rapidly reroute user connections. In the second phase, a distributed optimization process is initiated to optimally reroute handed-off connections. In this paper, we address various control issues related to signaling and implementation of such a scheme including how to achieve optimal paths. We analytically calculate and study the handoff blocking probability and the bandwidth requirement for the reserved virtual paths. We also study the impact of processing and signaling load due to the second-phase route optimization. Both ATM CBR and VBR traffic types were considered for mobile user connections