modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.

Modified nucleic acids have surged as a popular therapeutic route, emphasizing the importance of nucleic acid research in drug discovery and development. Beyond well-known RNA vaccines, antisense oligonucleotides and aptamers can incorporate various modified nucleic acids to target specific biomolecules for various therapeutic activities. Molecular dynamics simulations can accelerate the design and development of these systems with noncanonical nucleic acids by observing intricate dynamic properties and relative stability on the all-atom level.

Influence of sea ice concentration, sex and chick age on foraging flexibility and success in an Arctic seabird.

Declining sea ice and increased variability in sea ice dynamics are altering Arctic marine food webs. Changes in sea ice dynamics and prey availability are likely to impact pagophilic (ice-dependent and ice-associated) species, such as thick-billed murres (), through changes in foraging behaviour and foraging success. At the same time, extrinsic factors, such as chick demand, and intrinsic factors, such as sex, are also likely to influence foraging behaviour and foraging success of adult murres.

An arctic breeding songbird overheats during intense activity even at low air temperatures.

Birds maintain some of the highest body temperatures among endothermic animals. Often deemed a selective advantage for heat tolerance, high body temperatures also limits birds' thermal safety margin before reaching lethal levels. Recent modelling suggests that sustained effort in Arctic birds might be restricted at mild air temperatures, which may require reductions in activity to avoid overheating, with expected negative impacts on reproductive performance.

An interspecific foraging association with polar bears increases foraging opportunities for avian predators in a declining Arctic seabird colony.

Interspecific foraging associations (IFAs) are biological interactions where two or more species forage in association with each other. Climate-induced reductions in Arctic sea ice have increased polar bear () foraging in seabird colonies, which creates foraging opportunities for avian predators. We used drone video of bears foraging within a common eider () colony on East Bay Island (Nunavut, Canada) in 2017 to investigate herring gull () foraging in association with bears.

van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.

Molecular dynamics simulations can be used in combination with experimental techniques to uncover the intricacies of biomolecular structure, dynamics, and the resulting interactions. However, many noncanonical nucleic acid structures have proven to be challenging to replicate in accurate agreement with experimental data, often attributed to known force field deficiencies. A common force field criticism is the handling of van der Waals (vdW) parameters, which have not been updated since the regular use of Ewald's methods became routine.