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

Structure and stability of chiral beta-tapes: a computational coarse-grained approach

We present two coarse-grained models of different levels of detail for the description of beta-sheet tapes obtained from equilibrium self-assembly of short rationally designed oligopeptides in solution. Here we only consider the case of the homopolymer oligopeptides with the identical sidegroups attached, in which the tapes have a helicoid surface with two equivalent sides. The influence of the chirality parameter on the geometrical characteristics, namely the diameter, inter-strand distance and pitch, of the tapes have been investigated. The two models are found to produceequivalent results suggesting a considerable degree of universality in conformations of the tapes.Comment: 24 pages, 5 PS figures. Accepted to J. Chem. Phy

The Development of New Casting Alloys Intended for Operation Under Extreme Conditions and Some Techniques of Making Castings From Them

The article studies new heat-resistant and wear resistant materials for operation under extreme conditions, especially in the power industry. The methods that improve the quality of a metal in metal castings through the influence of alloying elements on its structure and properties have been considered. These methods are very effective for reducing the tendency of a metal to form a coarse–grained structure. The paper describes optimal techniques for melting special alloys in induction and electric furnaces. A set of rules for the selection of a melting temperature before pouring a metal into the casting forms depending on the dimensions, wall thickness, geometry of castings have been determined. The behavior of new alloys under the conditions of high temperatures, aggressive environments has been studied.It has been established that heat–resistant Cr–Al steels exhibit high heat resistance and wear resistance properties; they 6–8 times surpass Cr–Ni steels in oxidation resistance. The proposed Cr–Mn cast iron processed in an integrated manner with REM (rare earth metals) and Ti is superior to a basic cast iron in conditions of a heavy wear. Numerous industrial trials confirm the usefulness of recommended new casting materials for use under extreme conditions

Superfluidity of identical fermions in an optical lattice: atoms and polar molecules

In this work, we discuss the emergence of $p$-wave superfluids of identical fermions in 2D lattices. The optical lattice potential manifests itself in an interplay between an increase in the density of states on the Fermi surface and the modification of the fermion-fermion interaction (scattering) amplitude. The density of states is enhanced due to an increase of the effective mass of atoms. In deep lattices, for short-range interacting atoms, the scattering amplitude is strongly reduced compared to free space due to a small overlap of wavefunctions of fermions sitting in the neighboring lattice sites, which suppresses the $p$-wave superfluidity. However, we show that for a moderate lattice depth there is still a possibility to create atomic $p$-wave superfluids with sizable transition temperatures. The situation is drastically different for fermionic polar molecules. Being dressed with a microwave field, they acquire a dipole-dipole attractive tail in the interaction potential. Then, due to a long-range character of the dipole-dipole interaction, the effect of the suppression of the scattering amplitude in 2D lattices is absent. This leads to the emergence of a stable topological $p_x+ip_y$ superfluid of identical microwave-dressed polar molecules.Comment: 14 pages, 4 figures; prepared for proceedings of the IV International Conference on Quantum Technologies (Moscow, July 12-16, 2017); the present paper summarizes the results of our studies arXiv:1601.03026 and arXiv:1701.0852

Empirical corrections and pair interaction energies in the fragment molecular orbital method

The energy and analytic gradient are developed for FMO combined with the Hartree-Fock method augmented with three empirical corrections (HF-3c). The auxiliary basis set approach to FMO is extended to perform pair interaction energy decomposition analysis. The FMO accuracy is evaluated for several typical systems including 3 proteins. Pair interaction energies computed with different approaches in FMO are compared for a water cluster and protein-ligand complexes.Comment: Revised version accepted in Chemical Physics Letter

Stabilization of Hypersonic Boundary Layers by Porous Coatings

A second-mode stability analysis has been performed for a hypersonic boundary layer on a wall covered by a porous coating with equally spaced cylindrical blind microholes. Massive reduction of the second mode amplification is found to be due to the disturbance energy absorption by the porous layer. This stabilization effect was demonstrated by experiments recently conducted on a sharp cone in the T-5 high-enthalpy wind tunnel of the Graduate Aeronautical Laboratories of the California Institute of Technology. Their experimental confirmation of the theoretical predictions underscores the possibility that ultrasonically absorptive porous coatings may be exploited for passive laminar flow control on hypersonic vehicle surfaces

Challenges in Open-air Microwave Quantum Communication and Sensing

Quantum communication is a holy grail to achieve secure communication among a set of partners, since it is provably unbreakable by physical laws. Quantum sensing employs quantum entanglement as an extra resource to determine parameters by either using less resources or attaining a precision unachievable in classical protocols. A paradigmatic example is the quantum radar, which allows one to detect an object without being detected oneself, by making use of the additional asset provided by quantum entanglement to reduce the intensity of the signal. In the optical regime, impressive technological advances have been reached in the last years, such as the first quantum communication between ground and satellites, as well as the first proof-of-principle experiments in quantum sensing. The development of microwave quantum technologies turned out, nonetheless, to be more challenging. Here, we will discuss the challenges regarding the use of microwaves for quantum communication and sensing. Based on this analysis, we propose a roadmap to achieve real-life applications in these fields.Comment: Long version of the article published in the Proceeding