Structure and stability of helices in square-well homopolymers

Recently, it has been demonstrated [Magee et al., Phys. Rev. Lett. 96, 207802 (2006)] that isolated, square-well homopolymers can spontaneously break chiral symmetry and freeze into helical structures at sufficiently low temperatures. This behavior is interesting because the square-well homopolymer is itself achiral. In this work, we use event-driven molecular dynamics, combined with an optimized parallel tempering scheme, to study this polymer model over a wide range of parameters. We examine the conditions where the helix structure is stable and determine how the interaction parameters of the polymer govern the details of the helix structure. The width of the square well (proportional to lambda) is found to control the radius of the helix, which decreases with increasing well width until the polymer forms a coiled sphere for sufficiently large wells. The helices are found to be stable for only a window of molecular weights. If the polymer is too short, the helix will not form. If the polymer is too long, the helix is no longer the minimum energy structure, and other folded structures will form. The size of this window is governed by the chain stiffness, which in this model is a function of the ratio of the monomer size to the bond length. Outside this window, the polymer still freezes into a locked structure at low temperature, however, unless the chain is sufficiently stiff, this structure will not be unique and is similar to a glassy state.Comment: Submitted to Physical Review

Public views on the donation and use of human biological samples in biomedical research: a mixed methods study

Objective A mixed methods study exploring the UK general public's willingness to donate human biosamples (HBSs) for biomedical research.<p></p> Setting Cross-sectional focus groups followed by an online survey.<p></p> Participants Twelve focus groups (81 participants) selectively sampled to reflect a range of demographic groups; 1110 survey responders recruited through a stratified sampling method with quotas set on sex, age, geographical location, socioeconomic group and ethnicity.<p></p> Main outcome measures (1) Identify participants’ willingness to donate HBSs for biomedical research, (2) explore acceptability towards donating different types of HBSs in various settings and (3) explore preferences regarding use and access to HBSs.<p></p> Results 87% of survey participants thought donation of HBSs was important and 75% wanted to be asked to donate in general. Responders who self-reported having some or good knowledge of the medical research process were significantly more likely to want to donate (p<0.001). Reasons why focus group participants saw donation as important included: it was a good way of reciprocating for the medical treatment received; it was an important way of developing drugs and treatments; residual tissue would otherwise go to waste and they or their family members might benefit. The most controversial types of HBSs to donate included: brain post mortem (29% would donate), eyes post mortem (35%), embryos (44%), spare eggs (48%) and sperm (58%). Regarding the use of samples, there were concerns over animal research (34%), research conducted outside the UK (35%), and research conducted by pharmaceutical companies (56%), although education and discussion were found to alleviate such concerns.<p></p> Conclusions There is a high level of public support and willingness to donate HBSs for biomedical research. Underlying concerns exist regarding the use of certain types of HBSs and conditions under which they are used. Improved education and more controlled forms of consent for sensitive samples may mitigate such concerns.<p></p&gt

Consent for the use of human biological samples for biomedical research: a mixed methods study exploring the UK public’s preferences

OBJECTIVE: A mixed-methods study exploring the UK general public's views towards consent for the use of biosamples for biomedical research.<p></p> SETTING: Cross-sectional population-based focus groups followed by an online survey.<p></p> PARTICIPANTS: 12 focus groups (81 participants) selectively sampled to reflect a range of demographic groups; 1110 survey responders recruited through a stratified sampling method with quotas set on sex, age, geographical location, socioeconomic group and ethnicity.<p></p> MAIN OUTCOME MEASURES: (1) Views on the importance of consent when donating residual biosamples for medical research; (2) preferences for opt-in or opt-out consent approaches and (3) preferences for different consent models.<p></p> RESULTS: Participants believed obtaining consent for use of residual biosamples was important as it was 'morally correct' to ask, and enabled people to make an active choice and retain control over their biosamples. Survey responders preferred opt-in consent (55%); the strongest predictor was being from a low socioeconomic group (OR 2.22, 95% CI 1.41 to 3.57, p=0.001) and having a religious affiliation (OR 1.36, 95% CI 1.01 to 1.81, p=0.04). Focus group participants had a slight preference for opt-out consent because by using this approach more biosamples would be available and facilitate research. Concerning preferred models of consent for research use of biosamples, survey responders preferred specific consent with recontact for each study for which their biosamples are eligible. Focus group participants preferred generic consent as it provided 'flexibility for researchers' and reduced the likelihood that biosamples would be wasted. The strongest predictor for preferring specific consent was preferring opt-in consent (OR 4.58, 95% CI 3.30 to 6.35, p=0.015) followed by non-'White' ethnicity (OR 2.94, 95% CI 1.23 to 7.14, p<0.001).<p></p> CONCLUSIONS: There is a preference among the UK public for ongoing choice and control over donated biosamples; however, increased knowledge and opportunity for discussion is associated with acceptance of less restrictive consent models for some people.<p></p&gt

Fluent temporal logic for discrete-time event-based models

Fluent model checking is an automated technique for verifying that an event-based operational model satisfies some state-based declarative properties. The link between the event-based and state-based formalisms is defined through fluents which are state predicates whose value are determined by the occurrences of initiating and terminating events that make the fluents values become true or false, respectively. The existing fluent temporal logic is convenient for reasoning about untimed event-based models but difficult to use for timed models. The paper extends fluent temporal logic with temporal operators for modelling timed properties of discrete-time event-based models. It presents two approaches that differ on whether the properties model the system state after the occurrence of each event or at a fixed time rate. Model checking of timed properties is made possible by translating them into the existing untimed framework. Copyright 2005 ACM

How much do disasters cost? A comparison of disaster cost estimates in Australia

Extreme weather events in Australia are common and a large proportion of the population are exposed to such events. Therefore, there is great interest as to how these events impact Australia's society and economy, which requires understanding the current and historical impact of disasters. Despite global efforts to record and cost disaster impacts, no standardised method of collecting and recording data retrospectively yet exists. The lack of standardisation in turn results in a range of different estimates of economic impacts. This paper examines five examples of aggregate disaster loss and impacts of natural disasters in Australia, and comparisons between them reveal significant data shortcomings. The reliability of data sources, and the methodology employed to analyse them can have significant impacts on conclusions regarding the overall cost of disasters, the relative costs of different hazards (disaster types), and the distribution of losses across Australian states. We highlight difficulties with time series comparisons, further complicated by the interdependencies of the databases. We reiterate the need for consistent and comparable data collection and analysis, to respond to the increasing frequency and severity of disasters in Australia