Critical Scales Govern the Mechanical Fragmentation Mechanisms of Biomolecular Assemblies

2013 ◽  
Vol 80 (6) ◽  
Author(s):  
Matthew Sullivan ◽  
Sinan Keten
Keyword(s):  
Impact Energy ◽  
Relative Magnitude ◽  
Size Scaling ◽  
Fragmentation Mechanisms ◽  
Critical Impact Velocity ◽  
Fibril Length ◽  
Dynamics Simulations ◽  
The Impact ◽  
Mechanical Fragmentation ◽  
Insight Into

Fragmentation mechanisms of peptide assemblies under shock deformation are studied using molecular dynamics simulations and are found to depend strongly on the relative magnitude of the shock front radius to the fibril length and the ratio of the impact energy to the fibril cohesive energy. The competition between size scaling of curvature and impact energy leads to a mechanism change at a critical impact velocity, developing a stark contrast in the size scaling of fragmentation at low and high strain rates. We show that the fragmentation mechanisms can be classified on the basis of the length and time scales of deformation and relaxation to provide new insight into experimental observations.

Conformational and aggregation properties of PffBT4T polymers: atomistic insight into the impact of alkyl-chain branching positions

2019 ◽  
Vol 7 (45) ◽  
pp. 14198-14204
Author(s):  
Lu Ning ◽  
Guangchao Han ◽  
Yuanping Yi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Alkyl Chain ◽  
Temperature Dependent ◽  
Chain Branching ◽  
Alkyl Chains ◽  
Dynamics Simulations ◽  
The Impact ◽  
Insight Into

The impact of the branching positions of alkyl chains on temperature dependent aggregation is rationalized by atomistic molecular dynamics simulations.

Structure, Dynamics, Receptor Binding, and Antibody Binding of Fully-glycosylated Full-length SARS-CoV-2 Spike Protein in a Viral Membrane

2020 ◽  
Author(s):  
Yeol Kyo Choi ◽  
Yiwei Cao ◽  
Martin Frank ◽  
Hyeonuk Woo ◽  
Sang-Jun Park ◽  
...  
Keyword(s):  
Receptor Binding ◽  
Vaccine Development ◽  
Accessible Surface Area ◽  
Full Length ◽  
S Protein ◽  
Viral Membrane ◽  
Accessible Surface ◽  
Dynamics Simulations ◽  
The Impact ◽  
Insight Into

ABSTRACTThe spike (S) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) mediates host cell entry by binding to angiotensin-converting enzyme 2 (ACE2), and is considered the major target for drug and vaccine development. We previously built fully-glycosylated full-length SARS-CoV-2 S protein models in a viral membrane including both open and closed conformations of receptor binding domain (RBD) and different templates for the stalk region. In this work, multiple μs-long all-atom molecular dynamics simulations were performed to provide deeper insight into the structure and dynamics of S protein, and glycan functions. Our simulations reveal that the highly flexible stalk is composed of two independent joints and most probable S protein orientations are competent for ACE2 binding. We identify multiple glycans stabilizing the open and/or closed states of RBD, and demonstrate that the exposure of antibody epitopes can be captured by detailed antibody-glycan clash analysis instead of a commonly-used accessible surface area analysis that tends to overestimate the impact of glycan shielding and neglect possible detailed interactions between glycan and antibody. Overall, our observations offer structural and dynamic insight into SARS-CoV-2 S protein and potentialize for guiding the design of effective antiviral therapeutics.

scholarly journals Hydroxymethyluracil modifications enhance the flexibility and hydrophilicity of double-stranded DNA

2015 ◽  
Vol 44 (5) ◽  
pp. 2085-2092 ◽  
Author(s):  
Spencer Carson ◽  
James Wilson ◽  
Aleksei Aksimentiev ◽  
Peter R. Weigele ◽  
Meni Wanunu
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Chemical Properties ◽  
Double Stranded Dna ◽  
Physico Chemical ◽  
Translocation Experiments ◽  
Dynamics Simulations ◽  
Regulatory Dna ◽  
The Impact ◽  
Insight Into

Abstract Oxidation of a DNA thymine to 5-hydroxymethyluracil is one of several recently discovered epigenetic modifications. Here, we report the results of nanopore translocation experiments and molecular dynamics simulations that provide insight into the impact of this modification on the structure and dynamics of DNA. When transported through ultrathin solid-state nanopores, short DNA fragments containing thymine modifications were found to exhibit distinct, reproducible features in their transport characteristics that differentiate them from unmodified molecules. Molecular dynamics simulations suggest that 5-hydroxymethyluracil alters the flexibility and hydrophilicity of the DNA molecules, which may account for the differences observed in our nanopore translocation experiments. The altered physico-chemical properties of DNA produced by the thymine modifications may have implications for recognition and processing of such modifications by regulatory DNA-binding proteins.

scholarly journals Impact of a motorcycle on cyclist aerodynamic drag in parallel and staggered arrangements

2021 ◽  
Vol 24 (1) ◽  
Author(s):  
Bert Blocken ◽  
Stefanie Gillmeier ◽  
Fabio Malizia ◽  
Thijs van Druenen
Keyword(s):  
Aerodynamic Drag ◽  
Television Broadcasting ◽  
Close Proximity ◽  
Parallel Arrangement ◽  
Staggered Arrangement ◽  
Computational Fluid Dynamics Simulations ◽  
Calm Weather ◽  
Dynamics Simulations ◽  
The Impact ◽  
Insight Into

AbstractCycling races contain a multitude of motorcycles for various activities including television broadcasting. During parts of the race, these motorcycles can ride in close proximity of cyclists. Earlier studies focused on the impact of a nearby motorcycle on cyclist drag for in-line arrangements. It was shown that not only a motorcycle in front of a cyclist but also a motorcycle closely behind a cyclist can substantially reduce cyclist drag. However, there appears to be no information in the scientific literature about the impact of the motorcycle on cyclist drag for parallel and staggered arrangements. This paper presents wind tunnel measurements of cyclist drag for 32 different parallel and staggered cyclist-motorcycle arrangements. It is shown that the parallel arrangement leads to a drag increase for the cyclist, in the range of 5 to about 10% for a lateral distance of 2 to 1 m. The staggered arrangement can lead to either a drag increase or a drag decrease, where the latter is about 2% for most positions analyzed. For one of the parallel arrangements, computational fluid dynamics simulations were performed to provide insight into the reasons for the drag increase. A cyclist power model was used to convert the drag changes into potential time gains or losses. Compared to a lone cyclist riding at a speed of 46.8 km/h (13 m/s) on level road in calm weather, the time loss by a drag increase of 10%, 4% and − 2% was 2.16, 0.76 s and − 0.80 s per km, respectively. These time differences are large enough to influence the outcome of cycling races.

scholarly journals Changing landscapes: Gay men in the west and northwest of Ireland

Sexualities ◽  
2020 ◽  
pp. 136346072098169
Author(s):  
Aidan McKearney
Keyword(s):  
Gay Men ◽  
Social Rights ◽  
Irish Society ◽  
Recent Past ◽  
Same Sex ◽  
Lgbt People ◽  
The Many ◽  
Northwest Region ◽  
The Impact ◽  
Insight Into

This article focuses on the experiences of gay men in the rural west and northwest region of Ireland, during a period of transformational social and political change in Irish society. These changes have helped facilitate new forms of LGBTQI visibility, and local radicalism in the region. Same-sex weddings, establishment of rural LGBT groups and marching under an LGBT banner at St Patricks Day parades would have been unthinkable in the recent past; but they are now becoming a reality. The men report continuing challenges in their lives as gay men in the nonmetropolitan space, but the emergence of new visibility, voice and cultural acceptance of LGBT people is helping change their lived experiences. The study demonstrates the impact of local activist LGBT citizens. Through their testimonies we can gain an insight into the many, varied and interwoven factors that have interplayed to create the conditions necessary for the men to: increasingly define themselves as gay to greater numbers of people in their localities; to embrace greater visibility and eschew strategies of silence; and aspire to a host of legal, political, cultural and social rights including same-sex marriage. Organic forms of visibility and local radicalism have emerged in the region and through an analysis of their testimonies we can see how the men continue to be transformed by an ever-changing landscape.

Double, triple or quadruple hits? Exploring the impact of cybercrime on victims in the Netherlands

2021 ◽  
pp. 026975802110106
Author(s):  
Raoul Notté ◽  
E.R. Leukfeldt ◽  
Marijke Malsch
Keyword(s):  
Public Opinion ◽  
Literature Review ◽  
The Netherlands ◽  
Public Discourse ◽  
Moral Judgments ◽  
Victim Blaming ◽  
High Prevalence ◽  
Different Types ◽  
The Impact ◽  
Insight Into

This article explores the impact of online crime victimisation. A literature review and 41 interviews – 19 with victims and 22 with experts – were carried out to gain insight into this. The interviews show that most impacts of online offences correspond to the impacts of traditional offline offences. There are also differences with offline crime victimisation. Several forms of impact seem to be specific to victims of online crime: the substantial scale and visibility of victimhood, victimisation that does not stop in time, the interwovenness of online and offline, and victim blaming. Victims suffer from double, triple or even quadruple hits; it is the accumulation of different types of impact, enforced by the limitlessness in time and space, which makes online crime victimisation so extremely invasive. Furthermore, the characteristics of online crime victimisation greatly complicate the fight against and prevention of online crime. Finally, the high prevalence of cybercrime victimisation combined with the severe impact of these crimes seems contradictory with public opinion – and associated moral judgments – on victims. Further research into the dominant public discourse on victimisation and how this affects the functioning of the police and victim support would be valuable.

scholarly journals Using syndromic measures of mortality to capture the dynamics of COVID-19 in Java, Indonesia, in the context of vaccination rollout

BMC Medicine ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Bimandra A. Djaafara ◽  
Charles Whittaker ◽  
Oliver J. Watson ◽  
Robert Verity ◽  
Nicholas F. Brazeau ◽  
...  
Keyword(s):  
Rural Areas ◽  
Vaccination Campaign ◽  
Control Measures ◽  
Additional Insight ◽  
Short Term ◽  
If Current ◽  
Vaccine Impact ◽  
Potential Impact ◽  
The Impact ◽  
Insight Into

Abstract Background As in many countries, quantifying COVID-19 spread in Indonesia remains challenging due to testing limitations. In Java, non-pharmaceutical interventions (NPIs) were implemented throughout 2020. However, as a vaccination campaign launches, cases and deaths are rising across the island. Methods We used modelling to explore the extent to which data on burials in Jakarta using strict COVID-19 protocols (C19P) provide additional insight into the transmissibility of the disease, epidemic trajectory, and the impact of NPIs. We assess how implementation of NPIs in early 2021 will shape the epidemic during the period of likely vaccine rollout. Results C19P burial data in Jakarta suggest a death toll approximately 3.3 times higher than reported. Transmission estimates using these data suggest earlier, larger, and more sustained impact of NPIs. Measures to reduce sub-national spread, particularly during Ramadan, substantially mitigated spread to more vulnerable rural areas. Given current trajectory, daily cases and deaths are likely to increase in most regions as the vaccine is rolled out. Transmission may peak in early 2021 in Jakarta if current levels of control are maintained. However, relaxation of control measures is likely to lead to a subsequent resurgence in the absence of an effective vaccination campaign. Conclusions Syndromic measures of mortality provide a more complete picture of COVID-19 severity upon which to base decision-making. The high potential impact of the vaccine in Java is attributable to reductions in transmission to date and dependent on these being maintained. Increases in control in the relatively short-term will likely yield large, synergistic increases in vaccine impact.

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