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 $18.3\pm 3.5$ kcal mol$^{-1}$ for MP2/cc-pVDZ and $19.3\pm 3.6$ 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

Equivalence of particle-particle random phase approximation correlation energy and ladder-coupled-cluster doubles

We present an analytical proof and numerical demonstrations of the equivalence of the correlation energy from particle-particle random phase approximation (pp-RPA) and ladder-couple-cluster-doubles (ladder-CCD). These two theories reduce to the identical algebraic matrix equation and correlation energy expressions, under the assumption that the pp-RPA equation is stable. The numerical examples illustrate that the correlation energy missed by pp-RPA in comparison with couple-cluster single and double is largely canceled out when considering reaction energies. This theoretical connection will be beneficial to future pp-RPA studies based on the well established couple cluster theory