BackgroundMarkov state models have been widely used to study conformational changes of biological macromolecules. These models are built from short timescale simulations and then propagated to extract long timescale dynamics. However, the solvent information in molecular simulations are often ignored in current methods, because of the large number of solvent molecules in a system and the indistinguishability of solvent molecules upon their exchange.MethodsWe present a solvent signature that compactly summarizes the solvent distribution in the high-dimensional data, and then define a distance metric between different configurations using this signature. We next incorporate the solvent information into the construction of Markov state models and present a fast geometric clustering algorithm which combines both the solute-based and solvent-based distances.ResultsWe have tested our method on several different molecular dynamical systems, including alanine dipeptide, carbon nanotube, and benzene rings. With the new solvent-based signatures, we are able to identify different solvent distributions near the solute. Furthermore, when the solute has a concave shape, we can also capture the water number inside the solute structure. Finally we have compared the performances of different Markov state models. The experiment results show that our approach improves the existing methods both in the computational running time and the metastability.ConclusionsIn this paper we have initiated an study to build Markov state models for molecular dynamical systems with solvent degrees of freedom. The methods we described should also be broadly applicable to a wide range of biomolecular simulation analyses.

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Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way.Publisher's statement: © 2016 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting /republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription. Abstract-Wireless sensor networks (WSNs) are regularly used in asset monitoring applications, where the location of an asset or assets must be kept private. Providing location privacy for such an asset is tantamount to protecting the location of a source node from an attacker who is attempting to locate it. Although no solution exists to provide source location privacy over an extended period, it has been shown that attackers can be sufficiently inhibited by prominent approaches that use either a phantom node, via which protocol messages are routed, or nodes assigned to be fake sources, each of which then broadcast fake messages. However, the applicability of fake source approaches to networks where location privacy must be maintained for multiple sources has yet to be considered. This paper addresses this issue by analysing a representative fake source algorithm in the context of multiple sources, presenting simulation results that demonstrate the shortcomings of the approach and identifying the underlying limitations to pave the way for the development of algorithms capable of accounting for multiple sources.

(2015) Assessing the performance of phantom routing on source location privacy in wireless sensor networks. In: 2015 IEEE 21st Pacific Rim International Symposium on Dependable Computing (PRDC), Zhangjiajie, China, 18-20 Nov 2015 Copies of full items can be used for personal research or study, educational, or not-for profit purposes without prior permission or charge. Provided that the authors, title and full bibliographic details are credited, a hyperlink and/or URL is given for the original metadata page and the content is not changed in any way.Publisher's statement: "© 2015 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting /republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works." A note on versions:The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP url' above for details on accessing the published version and note that access may require a subscription.For more information, please contact the WRAP Team at: publications@warwick.ac.uk Assessing the Performance of Phantom Routing on Source Location Privacy in Wireless Sensor NetworksChen Gu, Matthew Bradbury, Arshad Jhumka, and Matthew Leeke Department of Computer Science, University of Warwick, Coventry, United Kingdom, CV4 7AL {cspmaj, bradbury, matt, arshad}@dcs.warwick.ac.uk Abstract-As wireless sensor networks (WSNs) have been applied across a spectrum of application domains, the problem of source location privacy (SLP) has emerged as a significant issue, particularly in safety-critical situations. In seminal work on SLP, phantom routing was proposed as an approach to addressing the issue. However, results presented in support of phantom routing have not included considerations for practical network configurations, omitting simulations and analyses with larger network sizes. This paper addresses this shortcoming by conducting an in-depth investigation of phantom routing under various network configurations. The results presented demonstrate that previous work in phantom routing does not generalise well to different network configurations. Specifically, under certain configurations, it is shown that the afforded SLP is reduced by a factor of up to 75.

As wireless sensor networks (WSNs) have been applied across a spectrum of application domains, the problem of source location privacy (SLP) has emerged as a significant issue, particularly in security-critical situations. In the seminal work on SLP, phantom routing was proposed as a viable approach to address SLP. However, recent work has shown some limitations of phantom routing such as poor performance with multiple sources. In this paper, we propose phantom walkabouts, a novel version and more general version of phantom routing, which performs phantom routes of variable lengths. Through extensive simulations we show that phantom walkabouts provides high SLP levels with a low message overhead and hence, low energy usage.

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The version presented here may differ from the published version or, version of record, if you wish to cite this item you are advised to consult the publisher's version. Please see the 'permanent WRAP URL' above for details on accessing the published version and note that access may require a subscription.

Source location privacy (SLP) is an important property for a large class of security-critical wireless sensor network (WSN) applications such as monitoring and tracking. In the seminal work on SLP, phantom routing was proposed as a viable approach to address SLP. However, recent work has shown some limitations of phantom routing such as poor data yield and low SLP. In this paper, we propose phantom walkabouts, a novel and more general version of phantom routing, which performs phantom routes of variable lengths. Through extensive simulations, we show that phantom walkabouts provides high SLP level than phantom routing under specific network configuration. KEYWORDSbiased random walk, phantom routing, phantom walkabouts, source location privacy, wireless sensor networks INTRODUCTIONA wireless sensor network (WSN) consists of a number of tiny devices, known as sensor nodes, that can sense different attributes of the environment and use radio signals to communicate among themselves. WSNs have enabled the development of many novel applications, including asset monitoring, 1 target tracking, 2 and environment control 3 among others, with low levels of intrusiveness. They are also expected to be deployed in safety and security-critical systems, including military 4 and medical services. 5 The communication protocols used in the WSNs must therefore meet a set of stringent security and privacy requirements, dependent on the application.Threats to privacy in monitoring applications can be considered along two dimensions, ie, (1) content-based threats and (2) context-based threats. Content-based privacy threats relate to use of the content of the messages broadcast by sensor nodes, such as an attacker gaining the ability to read an eavesdropped encrypted message. There has been much research addressing the issue of providing content privacy, eg, SPINS, 6 with most efforts in this area focusing on the use of cryptographic techniques. On the other hand, context-based privacy threats focus on the context in which messages are broadcast and how information can be observed or inferred by attackers. Context is a multi-attribute concept that encompasses situational aspects of broadcast messages, including environmental and temporal information.It is often desirable for the source of sensed information to be kept private in a WSN. For example, in a military application, a soldier transmitting messages may unintentionally disclose their location, even when encryption is used. Another example is during the monitoring of endangered species where poachers may be tempted to infer the location of the animal to capture it. Real world examples include monitoring badgers 2 and the WWF's Wildlife Crime Technology Report, 7 both of which would likely benefit from a context-based security measure. In this paper, we focus on protecting the source location.Techniques that protect this source location are said to provide source location privacy (SLP). SLP is important in many application domains, though it is of utmost concern in security-critica...