相关论文: Proton Dynamics in Protein Mass Spectrometry

The dynamic behavior of a partially wetting polymer droplet driven over a nanostructured interface is studied using molecular dynamics simulations. We consider the bead-spring model to represent a polymeric liquid that partially wets a…

We investigated the translation of a protein through model nanopores using coarse-grained (CG) non-equilibrium molecular dynamics (NEMD) simulations and compared the mobilities with those obtained from previous coarse-grained equilibrium…

An exact approach to compute physical properties for general multi-electronic-state (MES) systems in thermal equilibrium is presented. The approach is extended from our recent progress on path integral molecular dynamics (PIMD) [J. Chem.…

We investigate proteins within heterogeneous cell membranes where non-equilibrium phenomena arises from spatial variations in concentration and temperature. We develop simulation methods building on non-equilibrium statistical mechanics to…

A key step in interpreting gas-phase ion mobility coupled with mass spectrometry (IM-MS) data for unknown structure prediction involves identifying the most favorable protonated structure. In the gas phase, the site of protonation is…

Only indirect evidence of the role of magnetic braking in regulating gravitational collapse and the formation of circumstellar disks was found from observational work, such as compact disk sizes and the launching of high-velocity collimated…

Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…

The growing interest for comparing protein internal dynamics owes much to the realization that protein function can be accompanied or assisted by structural fluctuations and conformational changes. Analogously to the case of functional…

Protein footprinting is a new methodology that is based on probing, typically with the use of mass spectrometry, of reactivity of different aminoacid residues to a modifying reagent. Data thus obtained allow one to make inferences about…

Predicting favorable protein-peptide binding events remains a central challenge in biophysics, with continued uncertainty surrounding how nonlocal effects shape the global energy landscape. Here, we introduce peripheral surface information…

We present new parametrisations of energy spectra of secondary particles, $\pi$-mesons, gamma-rays, electrons and neutrinos, produced in inelastic proton-proton collisions. The simple analytical approximations based on imulations of…

The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…

Imaging the structure and observing the dynamics of isolated proteins using single-particle X-ray diffractive imaging (SPI) is one of the potential applications of X-ray free-electron lasers (XFELs). Currently, SPI experiments on isolated…

We employ an isospin dependent version of the QMD transport model to study the influence of the isospin dependent part of the nuclear matter equation of state and in-medium nucleon-nucleon cross-sections on the dynamics of heavy-ion…

We present a study of the physical plasma parameters such as electron temperature, electron density, column depth and filling factors in the moss regions and their variability over a short (an hour) and a long period (5 consecutive days) of…

The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…

Many aspects of the study of protein folding and dynamics have been affected by the recent advances in machine learning. Methods for the prediction of protein structures from their sequences are now heavily based on machine learning tools.…

In order to understand the physical processes of nanopore experiments at the molecular level, microscopic information from molecular dynamics is greatly needed. Coarse-grained models are a good alternative to classical all-atom models since…

It is now well established that materials are stronger when their dimensions are reduced to submicron scale. However, what happens at dimensions such as a few tens of nanometers or lower remains largely unknown, with conflicting reports on…