A network model for field and quenched disorder effects in artificial spin ice

We have performed a systematic study of the effects of field strength and quenched disorder on the driven dynamics of square artificial spin ice. We construct a network representation of the configurational phase space, where nodes represent the microscopic configurations and a directed link between node i and node j means that the field may induce a transition between the corresponding configurations. In this way, we are able to quantitatively describe how the field and the disorder affect the connectedness of states and the reversibility of dynamics. In particular, we have shown that for optimal field strengths, a substantial fraction of all states can be accessed using external driving fields, and this fraction is increased by disorder. We discuss how this relates to control and potential information storage applications for artificial spin ices

A Signature in HIV-1 Envelope Leader Peptide Associated with Transition from Acute to Chronic Infection Impacts Envelope Processing and Infectivity

Mucosal transmission of the human immunodeficiency virus (HIV) results in a bottleneck in viral genetic diversity. Gnanakaran and colleagues used a computational strategy to identify signature amino acids at particular positions in Envelope that were associated either with transmitted sequences sampled very early in infection, or sequences sampled during chronic infection. Among the strongest signatures observed was an enrichment for the stable presence of histidine at position 12 at transmission and in early infection, and a recurrent loss of histidine at position 12 in chronic infection. This amino acid lies within the leader peptide of Envelope, a region of the protein that has been shown to influence envelope glycoprotein expression and virion infectivity. We show a strong association between a positively charged amino acid like histidine at position 12 in transmitted/founder viruses with more efficient trafficking of the nascent envelope polypeptide to the endoplasmic reticulum and higher steady-state glycoprotein expression compared to viruses that have a non-basic position 12 residue, a substitution that was enriched among viruses sampled from chronically infected individuals. When expressed in the context of other viral proteins, transmitted envelopes with a basic amino acid position 12 were incorporated at higher density into the virus and exhibited higher infectious titers than did non-signature envelopes. These results support the potential utility of using a computational approach to examine large viral sequence data sets for functional signatures and indicate the importance of Envelope expression levels for efficient HIV transmission