198,584 research outputs found
Solid-state amorphization of Cu nanolayers embedded in a Cu64Zr36 glass
Solid-state amorphization of crystalline copper nanolayers embedded in a
Cu64Zr36 metallic glass is studied by molecular dynamics simulations for
different orientations of the crystalline layer. We show that solid-state
amorphization is driven by a reduction of interface energy, which compensates
the bulk excess energy of the amorphous nanolayer with respect to the
crystalline phase up to a critical layer thickness. A simple thermodynamic
model is derived, which describes the simulation results in terms of
orientation-dependent interface energies. Detailed analysis reveals the
structure of the amorphous nanolayer and allows a comparison to a quenched
copper melt, providing further insights into the origin of excess and interface
energy.Comment: 16 pages, 18 figure
Kinetic distance and kinetic maps from molecular dynamics simulation
Characterizing macromolecular kinetics from molecular dynamics (MD)
simulations requires a distance metric that can distinguish
slowly-interconverting states. Here we build upon diffusion map theory and
define a kinetic distance for irreducible Markov processes that quantifies how
slowly molecular conformations interconvert. The kinetic distance can be
computed given a model that approximates the eigenvalues and eigenvectors
(reaction coordinates) of the MD Markov operator. Here we employ the
time-lagged independent component analysis (TICA). The TICA components can be
scaled to provide a kinetic map in which the Euclidean distance corresponds to
the kinetic distance. As a result, the question of how many TICA dimensions
should be kept in a dimensionality reduction approach becomes obsolete, and one
parameter less needs to be specified in the kinetic model construction. We
demonstrate the approach using TICA and Markov state model (MSM) analyses for
illustrative models, protein conformation dynamics in bovine pancreatic trypsin
inhibitor and protein-inhibitor association in trypsin and benzamidine
Low temperature heat capacity of severely deformed metallic glass
The low temperature heat capacity of amorphous materials reveals a
low-frequency enhancement (boson peak) of the vibrational density of states, as
compared with the Debye law. By measuring the low-temperature heat capacity of
a Zr-based bulk metallic glass relative to a crystalline reference state, we
show that the heat capacity of the glass is strongly enhanced after severe
plastic deformation by high-pressure torsion, while subsequent thermal
annealing at elevated temperatures leads to a significant reduction. The
detailed analysis of corresponding molecular dynamics simulations of an
amorphous Zr-Cu glass shows that the change in heat capacity is primarily due
to enhanced low-frequency modes within the shear band region.Comment: 5 pages, 2 figure
Ab initio molecular dynamics study of collective excitations in liquid HO and DO: Effect of dispersion corrections
The collective dynamics in liquid water is an active research topic
experimentally, theoretically and via simulations. Here, ab initio molecular
dynamics simulations are reported in heavy and ordinary water at temperature
323.15 K, or 50C. The simulations in heavy water were performed both
with and without dispersion corrections. We found that the dispersion
correction (DFT-D3) changes the relaxation of density-density time correlation
functions from a slow, typical of a supercooled state, to exponential decay
behaviour of regular liquids. This implies an essential reduction of the
melting point of ice in simulations with DFT-D3. Analysis of longitudinal (L)
and transverse (T) current spectral functions allowed us to estimate the
dispersions of acoustic and optic collective excitations and to observe the L-T
mixing effect. The dispersion correction shifts the L and T optic (O) modes to
lower frequencies and provides by almost thirty per cent smaller gap between
the longest-wavelength LO and TO excitations, which can be a consequence of a
larger effective high-frequency dielectric permittivity in simulations with
dispersion corrections. Simulation in ordinary water with the dispersion
correction results in frequencies of optic excitations higher than in DO,
and in a long-wavelength LO-TO gap of 24 ps (127 cm).Comment: 14 pages, 9 figure
Hydration effects turn a highly stretched polymer from an entropic into an energetic spring
Polyethylene glycol (PEG) is a structurally simple and nontoxic water-soluble polymer that is widely used in medical and pharmaceutical applications as molecular linker and spacer. In such applications, PEG’s elastic response against conformational deformations is key to its function. According to text-book knowledge, a polymer reacts to the stretching of its end-to-end separation by a decrease in entropy that is due to the reduction of available conformations, which is why polymers are commonly called entropic springs. By a combination of single-molecule force spectroscopy experiments with molecular dynamics simulations in explicit water, we show that entropic hydration effects almost exactly compensate the chain conformational entropy loss at high stretching. Our simulations reveal that this entropic compensation is due to the stretching-induced release of water molecules that in the relaxed state form double hydrogen bonds with PEG. As a consequence, the stretching response of PEG is predominantly of energetic, not of entropic, origin at high forces and caused by hydration effects, while PEG backbone deformations only play a minor role. These findings demonstrate the importance of hydration for the mechanics of macromolecules and constitute a case example that sheds light on the antagonistic interplay of conformational and hydration degrees of freedom
Active-site protein dynamics and solvent accessibility in native<i>Achromobacter cycloclastes</i>copper nitrite reductase
Microbial nitrite reductases are denitrifying enzymes that are a major component of the global nitrogen cycle. Multiple structures measured from one crystal (MSOX data) of copper nitrite reductase at 240 K, together with molecular-dynamics simulations, have revealed protein dynamics at the type 2 copper site that are significant for its catalytic properties and for the entry and exit of solvent or ligands to and from the active site. Molecular-dynamics simulations were performed using different protonation states of the key catalytic residues (AspCATand HisCAT) involved in the nitrite-reduction mechanism of this enzyme. Taken together, the crystal structures and simulations show that the AspCATprotonation state strongly influences the active-site solvent accessibility, while the dynamics of the active-site `capping residue' (IleCAT), a determinant of ligand binding, are influenced both by temperature and by the protonation state of AspCAT. A previously unobserved conformation of IleCATis seen in the elevated temperature series compared with 100 K structures. DFT calculations also show that the loss of a bound water ligand at the active site during the MSOX series is consistent with reduction of the type 2 Cu atom.</jats:p
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