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Application of a significantly large bias voltage to small Bi2Sr2CaCu2O8+x mesa structures leads to persistent doping of the mesas. Here we employ this effect for analysis of the doping dependence of the electronic spectra of Bi-2212 single…
We report the first six-dimensional quantum dynamical calculations of dissociative adsorption and associative desorption. Using a potential energy surface obtained by density functional theory calculations, we show that the initial decrease…
We have studied dense hydrogen and deuterium experimentally up to 320 GPa and using ab initio molecular dynamic (MD) simulations up to 370 GPa between 250 and 300 K. Raman and optical absorption spectra show significant anharmonic and…
We report the splitting of an oscillating DNA circuit into $\sim 700$ droplets with picoliter volumes. Upon incubation at constant temperature, the droplets display sustained oscillations that can be observed for more than a day.…
The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an…
Inhibitory neurons play a crucial role in maintaining persistent neuronal activity. Although connected extensively through electrical synapses (gap-junctions), these neurons also exhibit interactions through chemical synapses in certain…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
Many cell membrane proteins that bind to actin form dynamic clusters driven by contractile flows generated by the actomyosin machinery at the cell cortex. Recent evidence suggests that a necessary condition for the generation of these…
We numerically investigate the competition between phase separation and dynamical arrest in a colloidal system interacting via a short ranged attractive potential. Equilibrium fluid configurations are quenched at two different temperatures…
We use systematic 8 ns ab initio molecular dynamics (AIMD) to study the structure and dynamics of water in bulk, and close to both hydrophobic and hydrophilic (carbonyl) groups of tetramethylurea (TMU). We observe crossovers in the…
The regulation of various cellular processes heavily relies on the protein complexes within a living cell, necessitating a comprehensive understanding of their three-dimensional structures to elucidate the underlying mechanisms. While…
The paradigm that the primary amino acid sequence prescribes structure and thus function has for a long time been central to the understanding of protein science. Though the theory is supported by the behaviour of most structured proteins,…
Liquid-liquid phase separation (LLPS) involving intrinsically disordered protein regions (IDRs) is a major physical mechanism for biological membraneless compartmentalization. The multifaceted electrostatic effects in these biomolecular…
Small molecule drug design hinges on obtaining co-crystallized ligand-protein structures. Despite AlphaFold2's strides in protein native structure prediction, its focus on apo structures overlooks ligands and associated holo structures.…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
The density of a protein molecule is a key property within a variety of experimental techniques. We present a computational method for determining protein mass density that explicitly incorporates hydration effects. Our approach uses…
We study the bifurcations of a set of nine nonlinear ordinary differential equations that describe the regulation of the cyclin-dependent kinase that triggers DNA synthesis and mitosis in the budding yeast, Saccharomyces cerevisiae. We show…
Intercalation of two-dimensional (2D) iron chalcogenides with molecular species requires disentangling electronic and structural contributions to understand the puzzling limit to superconducting transition temperature ($T_c$) at the…
Using computer simulations, we identify the mechanisms causing aggregation and structural arrest of colloidal suspensions interacting with a short-ranged attraction at moderate and high densities. Two different non-ergodicity transitions…
The low-frequency collective vibrational modes in proteins as well as the protein-water interface have been suggested as dominant factors controlling the efficiency of biochemical reactions and biological energy transport. It is thus…