Related papers: Proton Dynamics in Protein Mass Spectrometry
Predicting enzyme kinetic parameters quantifies how efficiently an enzyme catalyzes a specific substrate under defined biochemical conditions. Canonical parameters such as the turnover number ($k_\text{cat}$), Michaelis constant…
A PDE-based model combining surface electromigration and wetting is developed for the analysis of morphological stability of ultrathin solid films. Adatom mobility is assumed anisotropic, and two directions of the electric field (parallel…
Protein-peptide interactions play essential roles in many cellular processes and their structural characterization is the major focus of current experimental and theoretical research. Two decades ago, it was proposed to employ the steered…
The prediction of protein interactions (CPIs) is crucial for the in-silico screening step in drug discovery. Recently, many end-to-end representation learning methods using deep neural networks have achieved significantly better performance…
We present plasma diagnostics of an EIT wave observed with high cadence in Hinode/EIS sit-and-stare spectroscopy and SDO/AIA imagery obtained during the HOP-180 observing campaign on 2011 February 16. At the propagating EIT wave front, we…
Although a vast amount of experimental information is available on the elongation, compression, and folding of proteins in biochemical processes, very little is known about the real structure and molecular dynamics of DNA at an atomic…
Complex plasma mixtures with three or more components are often encountered in astrophysics or in inertial confinement fusion (ICF) experiments. For mixtures containing species with large differences in atomic number Z, the modeling needs…
Using finite temperature Raman spectroscopy, we investigate the electron-phonon interactions (EPI) and phonon-phonon scattering dynamics in the Dirac semimetal Cd3As2 in different fre quency regimes. Strong softening of the Raman shifts…
Isothermal-isobaric molecular dynamics simulations are used to examine the microscopic structure and some properties of water-methanol liquid mixture. The TIP4P/2005 and SPC/E water models are combined with the united atom TraPPE and the…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
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,…
Phi-values are experimental measures of how the kinetics of protein folding is changed by single-site mutations. Phi-values measure energetic quantities, but are often interpreted in terms of the structures of the transition state ensemble.…
It is demonstrated that the performance of the self-modulated proton driver plasma wakefield accelerator (SM-PDPWA) is strongly affected by the reduced phase velocity of the plasma wave. Using analytical theory and particle-in-cell…
Structural transformations at interfaces are of profound fundamental interest as complex examples of phase transitions in low-dimensional systems. Despite decades of extensive research, no compelling evidence exists for structural…
The molecular arrangement of lipids and proteins within biomembranes and monolayers gives rise to complex film morphologies as well as regions of distinct electrical surface potential, topographical and electrostatic nanoscale domains. To…
We study the effect of plasma composition on the dynamics and morphology of the relativistic astrophysical jets. Our work is based on a relativistic total variation diminishing (TVD) simulation code. We use a relativistic equation of state…
We study the compression and extension dynamics of a DNA-like polymer interacting with non-DNA binding and DNA-binding proteins, by means of computer simulations. The geometry we consider is inspired by recent experiments probing the…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Ni-doped MoS$_2$ is a layered material with useful tribological, optoelectronic, and catalytic properties. Experiment and theory on doped MoS$_2$ has focused mostly on monolayers or finite particles: theoretical studies of bulk Ni-doped…
Dynamics of pseudoscalar mesons ($\pi$, $\eta$, $K$ and $\overline{K}$ ) and hyperons ($\Lambda$ and $\Sigma$) produced in heavy-ion collisions near threshold energies has been investigated within the Lanzhou quantum molecular dynamics…