2,375 research outputs found
Mapping Enzymatic Catalysis using the Effective Fragment Molecular Orbital Method: Towards all ab initio Biochemistry
We extend the Effective Fragment Molecular Orbital (EFMO) method to the
frozen domain approach where only the geometry of an active part is optimized,
while the many-body polarization effects are considered for the whole system.
The new approach efficiently mapped out the entire reaction path of chorismate
mutase in less than four days using 80 cores on 20 nodes, where the whole
system containing 2398 atoms is treated in the ab initio fashion without using
any force fields. The reaction path is constructed automatically with the only
assumption of defining the reaction coordinate a priori. We determine the
reaction barrier of chorismate mutase to be kcal mol for
MP2/cc-pVDZ and for MP2/cc-pVTZ in an ONIOM approach using
EFMO-RHF/6-31G(d) for the high and low layers, respectively.Comment: SI not attache
Infrared limit in external field scattering
Scattering of electrons/positrons by external classical electromagnetic wave
packet is considered in infrared limit. In this limit the scattering operator
exists and produces physical effects, although the scattering cross-section is
trivial.Comment: 12 pages; published version; minor corrections; comments adde
Hybrid RHF/MP2 geometry optimizations with the Effective Fragment Molecular Orbital Method
The frozen domain effective fragment molecular orbital method is extended to
allow for the treatment of a single fragment at the MP2 level of theory. The
approach is applied to the conversion of chorismate to prephenate by chorismate
mutase, where the substrate is treated at the MP2 level of theory while the
rest of the system is treated at the RHF level. MP2 geometry optimization is
found to lower the barrier by up to 3.5 kcal/mol compared to RHF optimzations
and ONIOM energy refinement and leads to a smoother convergence with respect to
the basis set for the reaction profile. For double zeta basis sets the increase
in CPU time relative to RHF is roughly a factor of two.Comment: 11 pages, 3 figure
Implicit self-consistent electrolyte model in plane-wave density-functional theory
The ab-initio computational treatment of electrochemical systems requires an
appropriate treatment of the solid/liquid interfaces. A fully quantum
mechanical treatment of the interface is computationally demanding due to the
large number of degrees of freedom involved. In this work, we describe a
computationally efficient model where the electrode part of the interface is
described at the density-functional theory (DFT) level, and the electrolyte
part is represented through an implicit solvation model based on the
Poisson-Boltzmann equation. We describe the implementation of the linearized
Poisson-Boltzmann equation into the Vienna Ab-initio Simulation Package (VASP),
a widely used DFT code, followed by validation and benchmarking of the method.
To demonstrate the utility of the implicit electrolyte model, we apply it to
study the surface energy of Cu crystal facets in an aqueous electrolyte as a
function of applied electric potential. We show that the applied potential
enables the control of the shape of nanocrystals from an octahedral to a
truncated octahedral morphology with increasing potential
Spectrum of Tendon Pathologies: Triggers, Trails and End-State
The biggest compartment of the musculoskeletal system is the tendons and ligaments. In particular, tendons are dense tissues connecting muscle to bone that are critical for the integrity, function and locomotion of this system. Due to the increasing age of our society and the overall rise in engagement in extreme and overuse sports, there is a growing prevalence of tendinopathies. Despite the recent advances in tendon research and due to difficult early diagnosis, a multitude of risk factors and vague understanding of the underlying biological mechanisms involved in the progression of tendon injuries, the toolbox of treatment strategies remains limited and non-satisfactory. This review is designed to summarize the current knowledge of triggers, trails and end state of tendinopathies
Charge density and electric charge in quantum electrodynamics
The convergence of integrals over charge densities is discussed in relation
with the problem of electric charge and (non-local) charged states in Quantum
Electrodynamics (QED). Delicate, but physically relevant, mathematical points
like the domain dependence of local charges as quadratic forms and the time
smearing needed for strong convergence of integrals of charge densities are
analyzed. The results are applied to QED and the choice of time smearing is
shown to be crucial for the removal of vacuum polarization effects responible
for the time dependence of the charge (Swieca phenomenon). The possibility of
constructing physical charged states in the Feynman-Gupta-Bleuler gauge as
limits of local states vectors is discussed, compatibly with the vanishing of
the Gauss charge on local states. A modification by a gauge term of the Dirac
exponential factor which yields the physical Coulomb fields from the
Feynman-Gupta-Bleuler fields is shown to remove the infrared divergence of
scalar products of local and physical charged states, allowing for a
construction of physical charged fields with well defined correlation functions
with local fields
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