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The intersection between dislocations and a Ag(111) surface has been studied using an interplay of scanning tunneling microscopy (STM) and molecular dynamics (MD). Whereas the STM provides atomically resolved information about the surface…
We demonstrate that endonuclease deficient Clustered Regularly Interspaced Short Palindromic Repeats CRISPR-associated Cas9 protein (dCas9) fused to the photo-convertible fluorescence protein monomeric mEos3.1 (dCas9-mEos3) can be used to…
Improving the detailed understanding of the underlying properties and functions of biomolecules has recently attracted growing interest, enabled by the possibility of real-space imaging of single, intact macromolecules using Scanning…
Observational studies of magnetic fields are vital as magnetic fields play a crucial role in various astrophysical processes, including star formation, accretion of matter, transport processes (e.g., transport of heat), and cosmic rays. We…
The functions of RNA pseudoknots (PKs), which are minimal tertiary structural motifs and an integral part of several ribozymes and ribonucleoprotein complexes, are determined by their structure, stability and dynamics. Therefore, it is…
We present a panoramic view of the utility of coarse-grained (CG) models to study folding and functions of proteins and RNA. Drawing largely on the methods developed in our group over the last twenty years, we describe a number of key…
Incorporating either rotation equivariance or scale equivariance into CNNs has proved to be effective in improving models' generalization performance. However, jointly integrating rotation and scale equivariance into CNNs has not been…
Oral squamous cell carcinomas (OSCC) are the 6th most common cancer and the diagnosis is often belated for a curative treatment. The reliable and early differentiation between healthy and diseased cells is the main aim of this study in…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
Cell stiffness is a key determinant of how cells deform, migrate, and adapt to mechanically restrictive environments, yet existing single-cell stiffness assays remain difficult to combine with molecular analysis and downstream functional…
We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic…
We propose a polymer model for the dynamics of chromatin replication in three dimensional space. Our simulations indicate that both immobile and tracking replisomes may self-assemble during the process, reconciling previous apparently…
Molecular Communications (MC) is a bio-inspired communication technique that uses molecules to encode and transfer information. Many efforts have been devoted to developing novel modulation techniques for MC based on various distinguishable…
Scanning Tunneling Microscopy (STM) is a cornerstone technique for visualizing the electronic density of states with atomic resolution (typically below 0.1 nm). While the field of view of most STM setups extends up to a few microns,…
Atomic Force Microscopy (AFM) is a widely employed tool for micro-/nanoscale topographic imaging. However, conventional AFM scanning struggles to reconstruct complex 3D micro-/nanostructures precisely due to limitations such as incomplete…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the…
Biological membranes constitute boundaries of cells and cell organelles. Physico-chemical mechanisms at the atomic scale are dictated by protein-lipid interaction strength, lipid composition, lipid distribution in the vicinity of the…
Intact-organism imaging of Drosophila larvae reveals and quantifies chromatin-aqueous phase separation. The chromatin can be organized near the lamina layer of the nuclear envelope, conventionally fill the nucleus, be organized centrally,…