Quantum Mechanical Description Research Articles

Molecular Docking Using Quantum Mechanical-Based Methods.

Computational methods are a powerful and consolidated tool in the early stage of the drug lead discovery process. Amongthese techniques, high-throughput molecular docking has proved to be extremely useful in identifying novel bioactive compounds within large chemical libraries. In the docking procedure, the predominant binding mode of each small molecule within a target binding site is assessed, and a docking score reflective of the likelihood of binding is assigned to them. These methods also shed light on how a given hit could be modified in order to improve protein-ligand interactions and are thus able to guide lead optimization. The possibility of reducing time and cost compared to experimental approaches made this technology highly appealing. Due to methodological developments and the increase of computational power, the application of quantum mechanical methods to study macromolecular systems has gained substantial attention in the last decade. A quantum mechanical description of the interactions involved in molecular association of biomolecules may lead to better accuracy compared to molecular mechanics, since there are many physical phenomena that cannot be correctly described within a classical framework, such as covalent bond formation, polarization effects, charge transfer, bond rearrangements, halogen bonding, and others, that require electrons to be explicitly accounted for. Considering the fact that quantum mechanics-based approaches in biomolecular simulation constitute an active and important field of research, we highlight in this work the recent developments of quantum mechanical-based molecular docking and high-throughput docking.

On the Attenuation of a Wave Packet in Limited Systems Filled With an Active Medium and Plasma

In the article, for limited system conditions that form the spatial structure of the field, the attenuation processes of wave packets of finite amplitude are considered. The line width of the wave field may be the result of the dissipative processes (in a quantum system it is inverse of the lifetime of energy levels) or the result of reactive processes (in classical waveguide systems this is the spectral width of the packet). In the case of filling the waveguide with an active two-level medium, a description is possible using a quasiclassical model of the interaction of the field and particles. In this case, the quantum-mechanical description of the medium is combined with the classical representation of the field. Here, the Rabi frequency plays an important role, which determines the probabilities of induced radiation or absorption of field quanta and the oscillatory change in population inversion (nutation). Depending on the relationship between the Rabi frequency and the line width of the wave packet, the process can change the nature of the field behavior. In strong fields or with a significant population inversion, the line width can be neglected, while the field energy density is quite high. In this case, one should expect noticeable nutations of population inversions with different frequencies corresponding to the local Rabi frequency in different regions of the waveguide, the interference of which will determine the oscillatory behavior of the wave field. At a low level of electric field intensity or a slight population inversion, the mode of changing the field amplitude becomes monotonic. Plasma field damping (Landau damping) is considered. The role of population inversion is assumed by a quantity proportional to the derivative with respect to velocity of the electron distribution function. If the spectral width of the packet is small, the process of wave attenuation acquires a characteristic oscillatory form due to the exchange of energy between the wave and the plasma electrons captured by its field. The attenuation of wide packets is almost monotonic with the formation of a characteristic “plateau” in the vicinity of the phase velocity of the wave on the electron velocity distribution function.

Microscopic Calculation of Fission Fragment Distributions in Actinides

The simulation of independent and cumulative yields requires precise knowledge of the initial conditions of the fission fragments immediately after scission. In this paper, we use a quantum-mechanical description of fission dynamics to extract the initial mass distribution of fission fragments for the neutron-induced fission of the two major actinides239Pu and235U, both for thermal fission and as a function of the incident neutron energy.

Entropic Mechanics: Towards a Stochastic Description of Quantum Mechanics

We consider a stochastic process which is (a) described by a continuous-time Markov chain on only short time-scales and (b) constrained to conserve a number of hidden quantities on long time-scales. We assume that the transition matrix of the Markov chain is given and the conserved quantities are known to exist, but not explicitly given. To study the stochastic dynamics we propose to use the principle of stationary entropy production. Then the problem can be transformed into a variational problem for a suitably defined action and with time-dependent Lagrange multipliers. We show that the stochastic dynamics can be described by a Schrodinger equation, with Lagrange multipliers playing the role of phases, whenever (a) the transition matrix is symmetric or the detailed balance condition is satisfied, (b) the system is not too far from the equilibrium and (c) the number of the conserved quantities is large.

An Approach towards Quantization of Non-Relativistic Open String Theory

For decades, scientists have worked relentlessly to move forward to see what lies beyond the third dimension and to find out if there is any existence of a unified theory to explain all the workings of the universe from sub-atomic to gigantic inhabitants of cosmos. This insurmountable task has been taken on by many over the last century or so until the emergence of “superstring theory” or “string theory” happened showcasing the fact that an answer seemed possible. From the concepts of a “string”, our ideation on this theory started. In this paper we strived to put forward that the concept of a vibrating one-dimensional microscopic object named “string” can be taken as a fundamental ingredient (in place of point particle) for developing non-relativistic quantum mechanics. Unlike point particle, we take a vibrating string as the quantum object & build a perfectly reasonable quantum mechanical description of the microscopic world. Our main objective in this paper to show that complete development of quantum mechanics is possible based on one dimensional open string.

Isotope effects in liquid water via deep potential molecular dynamics

A comprehensive microscopic understanding of ambient liquid water is a major challenge for ab initio simulations as it simultaneously requires an accurate quantum mechanical description of the underlying potential energy surface (PES) as well as extensive sampling of configuration space. Due to the presence of light atoms (e.g. or ), nuclear quantum fluctuations lead to observable changes in the structural properties of liquid water (e.g. isotope effects), and therefore provide yet another challenge for ab initio approaches. In this work, we demonstrate that the combination of dispersion-inclusive hybrid density functional theory (DFT), the Feynman discretised path-integral (PI) approach, and machine learning (ML) constitutes a versatile ab initio based framework that enables extensive sampling of both thermal and nuclear quantum fluctuations on a quite accurate underlying PES. In particular, we employ the recently developed deep potential molecular dynamics (DPMD) model – a neural-network representation of the ab initio PES – in conjunction with a PI approach based on the generalised Langevin equation (PIGLET) to investigate how isotope effects influence the structural properties of ambient liquid and . Through a detailed analysis of the interference differential cross sections as well as several radial and angular distribution functions, we demonstrate that this approach can furnish a semi-quantitative prediction of these subtle isotope effects.

Modeling state-selective photodetachment in cold ion traps: Rotational state "crowding" in small anions.

Using accurate ab initio calculations of the interaction forces, we employ a quantum mechanical description of the collisional state-changing processes that occur in a cold ion trap with He as a buffer gas. We generate the corresponding inelastic rates for rotational transitions involving three simple molecular anions OH-(1Σ), MgH-(1Σ), and C2H-(1Σ) colliding with the helium atoms of the trap. We show that the rotational constants of these molecular anions are such that within the low-temperature regimes of a cold ion trap (up to about 50 K), a different proportion of molecular states are significantly populated when loading helium as a buffer gas in the trap. By varying the trap operating conditions, population equilibrium at the relevant range of temperatures is reached within different time scales. In the modeling of the photodetachment experiments, we analyze the effects of varying the chosen values for photodetachment rates as well as the laser photon fluxes. Additionally, the changing of the collision dynamics under different buffer gas densities is examined and the best operating conditions, for the different anions, for yielding higher populations of specific rotational states within the ion traps are extracted. The present modeling thus illustrates possible preparation of the trap conditions for carrying out more efficiently state-selected experiments with the trapped anions.

Temporal and spatially resolved imaging of the correlated nuclear-electronic dynamics and of the ionized photoelectron in a coherently electronically highly excited vibrating LiH molecule.

Few-cycle ultrashort IR pulses allow excitation of coherently coupled electronic states toward steering nuclear motions in molecules. We include in the Hamiltonian the excitation process using an IR pulse of a definite phase between its envelope and carrier wave and provide a quantum mechanical description of both multiphoton excitation and ionization. We report on the interplay between these two processes in shaping the ensuing coupled electronic-nuclear dynamics in both the neutral excited electronic states and the cationic states of the diatomic molecule LiH. The dynamics is described by solving numerically the time-dependent Schrodinger equation at nuclear grid points using the partitioning technique with a subspace of ten coupled bound states and a subspace of discretized continuous states for the photoionization continua. We show that the coherent dynamics in the neutral subspace is strongly affected by the amplitude exchanges with the ionization continua during the pulse, as well as by the onset of nuclear motion. The coupling to the cation and the resulting ionization do not preclude the control of the motion in the neutral through control of the carrier-envelope phase. Our methodology provides visualization in space and in time not only of the entangled vibronic wave packet in the neutral states but also of the wave packet of the outgoing photoelectron. Thereby, we can spatially and temporally follow the dynamics of the outgoing and bound electrons during the pulse and the nuclear motion in the bound subspace while moving through nonadiabatic coupling regions after the pulse.

Relativistic quantum-mechanical description of twisted paraxial electron and photon beams

The analysis of twisted (vortex) paraxial photons and electrons is fulfilled in the framework of relativistic quantum mechanics. The use of the Foldy-Wouthuysen representation radically simplifies a description of relativistic electrons and clarifies fundamental properties of twisted particles. It is demonstrated that the twisted photon defined by the Laguerre-Gauss wave function is luminal. Its apparent subluminality takes place because the photon energy is contributed by the hidden transversal motion while the average transversal momentum vanishes. Nevertheless, the Laguerre-Gauss photon can be self-consistently modeled by a subluminal centroid with a nonzero kinematic (Lorentz-invariant) mass. An applicability of this model is a consequence of independence of centroid parameters from the longitudinal coordinate. All twisted and untwisted Laguerre-Gauss modes are subliminal. The Laguerre-Gauss electron has similar properties. The new effect of a quantization of the velocity and mass of the Laguerre-Gauss photon and electron is predicted. This effect is observable for the photon. The twisted photon and electron modeled by the centroids are considered in the general noninertial frame. Their inertial masses coinciding with kinematic ones are determined. The orbital magnetic moment of the Laguerre-Gauss electron does not depend on the radial quantum number.

Volt-ampere characteristics of porcine retinal Müller cell intermediate filaments

In the current study we reported current-voltage (I/V) characteristics of Müller cell (MC) intermediate filaments (IFs) isolated from porcine retina. It was found that the measured I/V dependences demonstrate behavior of a semiconductor in contact with metal (Au) electrodes. The analysis of the temperature dependence of the experimental I/V curves produced estimates of the parameter values characterizing the electrical conductivity properties of the studied MC IFs. The I/V characteristics and the parameter values allowed to describe the MC IFs as a semiconducting material. The observed properties clarify the mechanism of high-contrast daylight vision of vertebrate eyes. This mechanism was extensively discussed earlier, and is directly dependent on the electric conductivity properties of MC IFs. Significance StatementRetinal cones and rods are physically connected to glial Müller cells by intermediate filaments (IFs). Electric conductivity of IFs allows for a simple quantum mechanical description of light energy transmission through the retina, providing a convincing mechanism that achieves high-contrast vision in vertebrate eyes. Note that classic light transmission is hindered by light scattering on the retinal structures. Electric conductivity of IFs also opens the possibility for energy exchange within and between other cell types by way of IFs and microtubules, and the possibility that such structures may be used for signaling e.g. in the nervous system.

Using Graph Partitioning for Scalable Distributed Quantum Molecular Dynamics

The simulation of the physical movement of multi-body systems at an atomistic level, with forces calculated from a quantum mechanical description of the electrons, motivates a graph partitioning problem studied in this article. Several advanced algorithms relying on evaluations of matrix polynomials have been published in the literature for such simulations. We aim to use a special type of graph partitioning to efficiently parallelize these computations. For this, we create a graph representing the zero–nonzero structure of a thresholded density matrix, and partition that graph into several components. Each separate submatrix (corresponding to each subgraph) is then substituted into the matrix polynomial, and the result for the full matrix polynomial is reassembled at the end from the individual polynomials. This paper starts by introducing a rigorous definition as well as a mathematical justification of this partitioning problem. We assess the performance of several methods to compute graph partitions with respect to both the quality of the partitioning and their runtime.

Bianchi type I, Schutz perfect fluid and evolutionary quantum cosmology

We study the classical and quantum cosmology of a universe in which the matter content is a perfect fluid and the background geometry is described by a Bianchi type I metric. To write the Hamiltonian of the perfect fluid we use the Schutz representation, in terms of which, after a particular gauge fixing, we are led to an identification of a clock parameter which may play the role of time for the corresponding dynamical system. In view of the classical cosmology, it is shown that the evolution of the universe represents a late time expansion coming from a big-bang singularity. We also consider the issue of quantum cosmology in the framework of the canonical Wheeler-DeWitt (WDW) equation. It is shown that the Schutz formalism leads to the introduction of a momentum that enters linearly into Hamiltonian. This means that the WDW equation takes the form of a Schr\"{o}dinger equation for the quantum-mechanical description of the model under consideration. We find the eigenfunctions and with the use of them construct the closed form expressions for the wave functions of the universe. By means of the resulting wave function we evaluate the expectation values and investigate the possibility of the avoidance of classical singularities due to quantum effects. We also look at the problem through Bohmian approach of quantum mechanics and while recovering the quantum solutions, we deal with the reason of the singularity avoidance by introducing quantum potential.

The problem of connection of observer’s mind with quantum-mechanical description of physical reality

Introduction: the study considers the problem of observer’s status during specific quantum-mechanical experiments, in which the empirical result directly depends on the participation of the experimenter's mind. Here the problem arises of the connection between the mind of the observer and the quantum-mechanical description of physical reality. The paper pays attention to modern trends in physics and philosophy devoted to the study of this phenomenon. Some aspects of the philosophical interpretation of the mind as a quantum mechanism are presented.Materials and Methods: the research materials demonstrate an overview of several common quantum-philosophical theories. Attempts have been made to search for the connection of quantum phenomena with the mechanisms of the functioning of human mind. The experimental background of quantum physics is demonstrated, providing material for analyzing the possibility of applying modern quantum theory to the question of identifying the relationship of the quantum approach and describing the problem of the influence of the observer’s mind on the result of a physical experiment.Results: the concept of quantum mechanics, taking into account the latest achievements and results of physics, philosophy and psychology, allows us to consider the mind of the observer as an integral part of the mechanism responsible for the formation of the surrounding physical reality. The anthropic principle of participation considered in the work gives the observer's mind a special role allowing to form a quantum-mechanical description of physical reality.Discussion and conclusions: it is shown that the mind of the observer plays an important role in quantum theory. Moreover, mind as a psychic phenomenon may be in fact identical with the quantum-mechanical concept of choosing an alternative. Given the fact that the brain's thought processes influence the measurement results, it can be assumed that mind changes quantum probabilities. This assumption allows us to take a different look at the concept of reality itself.

Circular Dichroism in Rotating Particles.

Light interaction with rotating nanostructures gives rise to phenemona as varied as optical torques and quantum friction. Surprisingly, the most basic optical response function of nanostructures undergoing rotation has not been clearly addressed so far. Here we reveal that mechanical rotation results in circular dichroism in optically isotropic particles, which show an unexpectedly strong dependence on the particle internal geometry. More precisely, particles with one-dimensionally confined electron motion in the plane perpendicular to the rotation axis, such as nanorings and nanocrosses, exhibit a splitting of 2Ω in the particle optical resonances, while compact particles, such as nanodisks and nanospheres, display weak circular dichroism. We base our findings on a quantum-mechanical description of the polarizability of rotating particles, incorporating the mechanical rotation by populating the particle electronic states according to the principle that they are thermally equilibrated in the rotating frame. We further provide insight into the rotational superradience effect and the ensuing optical gain, originating in population inversion as regarded from the lab frame, in which the particle is out of equilibrium. Surprisingly, we find the optical frequency cutoff for superradiance to deviate from the rotation frequency Ω. Our results unveil a rich, unexplored phenomenology of light interaction with rotating objects, which might find applications in various fields, such as optical trapping and sensing.

Laser-driven quantum magnonics and terahertz dynamics of the order parameter in antiferromagnets

The impulsive generation of two-magnon modes in antiferromagnets by femtosecond optical pulses, so-called femto-nanomagnons, leads to coherent longitudinal oscillations of the antiferromagnetic order parameter that cannot be described by a thermodynamic Landau-Lifshitz approach. We argue that this dynamics is triggered as a result of a laser-induced modification of the exchange interaction. In order to describe the oscillations we have formulated a quantum mechanical description in terms of magnon pair operators and coherent states. Such an approach allowed us to} derive an effective macroscopic equation of motion for the temporal evolution of the antiferromagnetic order parameter. An implication of the latter is that the photo-induced spin dynamics represents a macroscopic entanglement of pairs of magnons with femtosecond period and nanometer wavelength. By performing magneto-optical pump-probe experiments with 10 femtosecond resolution in the cubic KNiF$_3$ and the uniaxial K$_2$NiF$_4$ collinear Heisenberg antiferromagnets, we observed coherent oscillations at the frequency of 22 THz and 16 THz, respectively. The detected frequencies as a function of the temperature ideally fit the two-magnon excitation up to the N\'eel point. The experimental signals are described as dynamics of magnetic linear dichroism due to longitudinal oscillations of the antiferromagnetic vector.

Probing intensity-field correlations of single-molecule surface-enhanced Raman-scattered light

In the context of the quantum-mechanical description of single-molecule surface-enhanced Raman scattering, intensity-field correlation measurements of photons emitted from a plasmonic cavity are explored, theoretically, using the technique of conditional homodyne detection. The inelastic interplay between plasmons and vibrations of a diatomic molecule placed inside the cavity can be manifested in phase-dependent third-order fluctuations of the light recorded by the aforesaid technique, allowing us to reveal signatures of non-classicality (indicatives of squeezing) of the outgoing Raman photons.

The computation of local stress in ab initio molecular simulations

Motivated by the increasingly more important role of ab initio molecular dynamics models in material simulations, this work focuses on the definition of local stress, when the forces are determined from quantum-mechanical (QM) descriptions. Two types of ab initio models, including the Born–Oppenheimer and Ehrenfest dynamics, are considered. In addition, formulas are derived for both tight-binding and real-space methods for the approximations of the QM models. The formulas are examined via comparisons with full ab initio molecular simulations.

Quantum Mechanical Description of Electrostatics Provides a Unified Picture of Catalytic Action Across Methyltransferases.

Methyl transferases (MTases) are a well-studied class of enzymes for which competing enzymatic enhancement mechanisms have been suggested, ranging from structural methyl group CH···X hydrogen bonds (HBs) to electrostatic- and charge-transfer-driven stabilization of the transition state (TS). We identified all Class I MTases for which reasonable resolution (<2.0 Å) crystal structures could be used to form catalytically competent ternary complexes for multiscale (i.e., quantum-mechanical/molecular-mechanical or QM/MM) simulation of the SN2 methyl transfer reaction coordinate. The four Class I MTases studied have both distinct functions (e.g., protein repair or biosynthesis) and substrate nucleophiles (i.e., C, N, or O). While CH···X HBs stabilize all reactant complexes, no universal TS stabilization role is found for these interactions in MTases. A consistent picture is instead obtained through analysis of charge transfer and electrostatics, wherein much of cofactor-substrate charge separation is maintained in the TS region, and electrostatic potential is correlated with substrate nucleophilicity (i.e., intrinsic reactivity).

Tunable spherical graphene surface plasmon amplification by stimulated emission of radiation

A structure is suggested for spasing. The presented surface plasmon amplification by stimulated emission of Radiation (SPASER) is made up of a graphene nanosphere, which supports localized surface plasmon modes, and a quantum dot array, acting as a gain medium. The gain medium is pumped by an external light source. Since all the plasmons are carried on a graphene platform, the structure features coherent surface plasmons with high confinement and large life time. All the structures are analyzed theoretically using full quantum mechanical description. The main advantage of the proposed SPASER is its simple tuning capability of changing graphene’s Fermi level, which is performed by either chemical doping in the manufacturing time or electrostatic gating. We suggest the utilization of the proposed SPASER for exciting coherent long-range surface plasmons on a graphene sheet. The near field of the SPASER couples to the surface plasmons on graphene sheet and compensates the large momentum mismatch between surface plasmons and photons.

Quantum-classical path integral with a harmonic treatment of the back-reaction.

The quantum-classical path integral (QCPI) provides a rigorous methodology for simulating condensed phase processes when a fully quantum mechanical description of a small subsystem is necessary. While full QCPI calculations have been shown to be feasible on parallel computing platforms, the large number of trajectory calculations required leads to computational cost that significantly exceeds that of classical molecular dynamics calculations. This paper describes the harmonic back-reaction (HBR) approximation to the QCPI expression, which reduces dramatically the computational cost by requiring a single classical trajectory from each initial condition. Test calculations on a model of strongly anharmonic oscillators show that the HBR treatment quantitatively reproduces the full QCPI results. The HBR-QCPI algorithm is applicable to a variety of condensed phase and biological systems with effort only somewhat greater than that of molecular dynamics simulations.