Anna Lappala
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View article: From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture
From 2D to 4D: a Containerized Workflow and Browser to Explore Dynamic Chromatin Architecture Open
Characterizing the physical organization of the genome is essential for understanding long-range gene regulation, chromatin compartmentalization, and epigenetic accessibility. Hi-C experiments generate two-dimensional (2D) genome-wide cont…
View article: Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in PermissiveLung Cells.
Human Coronavirus Infection Reorganizes Spatial Genomic Architecture in PermissiveLung Cells. Open
Chromatin conformation capture followed by next-generation sequencing in combination with large-scale polymer simulations (4DHiC) produces detailed information on genomic loci interactions, allowing for the interrogation of 3D spatial geno…
View article: Cooperative Motions and Topology-Driven Dynamical Arrest in Prime Knots
Cooperative Motions and Topology-Driven Dynamical Arrest in Prime Knots Open
Knots are entangled structures that cannot be untangled without a cut. Topological stability of knots is one of the many examples of their important properties that can be used in information storage and transfer. Knot dynamics is importan…
View article: Revealing RCOR2 as a regulatory component of nuclear speckles
Revealing RCOR2 as a regulatory component of nuclear speckles Open
Background Nuclear processes such as transcription and RNA maturation can be impacted by subnuclear compartmentalization in condensates and nuclear bodies. Here we characterize the nature of nuclear granules formed by REST corepressor 2 (R…
View article: Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome
Four-dimensional chromosome reconstruction elucidates the spatiotemporal reorganization of the mammalian X chromosome Open
Significance Breakthrough technological advances such as Hi-C have enabled large-scale sequencing of pairwise genomic contacts. However, translating the 2D contacts to 3D spatial models remains challenging. Here we develop the “4DHiC” mode…
View article: Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail
Modeling the Influenza A NP-vRNA-Polymerase Complex in Atomic Detail Open
Seasonal flu is an acute respiratory disease that exacts a massive toll on human populations, healthcare systems and economies. The disease is caused by an enveloped Influenza virus containing eight ribonucleoprotein (RNP) complexes. Each …
View article: Mapping the body’s battle with Ebola and Zika
Mapping the body’s battle with Ebola and Zika Open
The viruses that cause Ebola and Zika, daunting diseases that inspire concern at every outbreak, share a strong similarity in how they first infiltrate a host’s cells. Through the computer modeling capabilities of Los Alamos National Labor…
View article: Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations
Scaling molecular dynamics beyond 100,000 processor cores for large‐scale biophysical simulations Open
The growing interest in the complexity of biological interactions is continuously driving the need to increase system size in biophysical simulations, requiring not only powerful and advanced hardware but adaptable software that can accomm…
View article: Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State
Structural Transition and Antibody Binding of EBOV GP and ZIKV E Proteins from Pre-Fusion to Fusion-Initiation State Open
Membrane fusion proteins are responsible for viral entry into host cells—a crucial first step in viral infection. These proteins undergo large conformational changes from pre-fusion to fusion-initiation structures, and, despite differences…
View article: Folding nano-scale paper cranes–the power of origami and kirigami in metamaterials
Folding nano-scale paper cranes–the power of origami and kirigami in metamaterials Open
Here, the ancient Japanese art of paper folding has influenced several branches of science from mathematics, physics to materials- and space sciences. One of the main advantages of origami is the precision of the folding mechanism that lea…
View article: Polymer glass transition occurs at the marginal rigidity point with connectivity z* = 4
Polymer glass transition occurs at the marginal rigidity point with connectivity z* = 4 Open
We re-examine the physical origin of the polymer glass transition from the point of view of marginal rigidity, which is achieved at a certain average number of mechanically active intermolecular contacts per monomer. In the case of polymer…
View article: Polymer glass transition as a local rigidity transition
Polymer glass transition as a local rigidity transition Open
We re-examine the physical origin of the polymer glass transition from the point of view of marginal rigidity, which is achieved above a certain number of intermolecular contacts. In the case of polymer chains in a melt / poor solvent, eac…
View article: Polymer glass transition occurs at the marginal rigidity point with connectivity z*=4
Polymer glass transition occurs at the marginal rigidity point with connectivity z*=4 Open
We re-examine the physical origin of the polymer glass transition from the point of view of marginal rigidity, which is achieved above a certain number of intermolecular contacts. In the case of polymer chains in a melt / poor solvent, eac…