Advanced Computer Graphics Aided Molecular Visualization and Manipulation Softwares: The Hierarchy of Research Methodologies

In the present day, the huge obstacles, and the major technical problems encountered by the teaching and research faculties, academicians, industrial specialists, laboratory demonstrators and instructors, fellow students and researchers, etc. are to adopt integrative approaches of demonstrating (learning) chemistry and chemical education, and the realistic ways of delivering (grasping) scientific materials articulately with graceful and effortless manner. Towards minimizing these challenges, various audio-visual tools and technologies, advanced computer aided molecular graphics, freely available electronic gadgets assisted chemistry and chemical education apps, human unreadable data reading and accessing softwares, etc. are being incorporated worldwide as the most indispensable physical and electronic means for successful professionalisms. This short article is essentially a collective report underscoring extraordinary approaches, incredible efforts, and innovative skills of the computer based chemical and molecular graphics towards illuminating intrinsic parts of the chemistry and chemical education, and revealing various aspects of the cutting -edge research. As their representatives, herein, the different type computer coding languages based graphical tools such as Molden, GaussView, Jmol, and Visual Molecular Dynamics (VMD) are referred, and elucidated their potential applications and remarkable attempts in the advancement of diverse areas of chemistry and chemical education. Beside this, the most essential graphical features, unique rendering abilities with magnificent views, splendid visualizing skills, awesome data accessing functionalities, etc. of each of them, and their invaluable roles for studying complex molecules, biomolecules, crystals, and the entire material assemblies as well as for investigating global and local molecular physicochemical properties are presented concisely with the special stresses on their relatively better and comparatively more applicable distinctive attributes explicitl

A scheme for entanglement extraction from a solid

Some thermodynamical properties of solids, such as heat capacity and magnetic susceptibility, have recently been shown to be linked to the amount of entanglement in a solid. However this entanglement may appear a mere mathematical artifact of the typical symmetrization procedure of many-body wave function in solid state physics. Here we show that this entanglement is physical demonstrating the principles of its extraction from a typical solid state system by scattering two particles off the system. Moreover we show how to simulate this process using present-day optical lattices technology. This demonstrates not only that entanglement exists in solids but also that it can be used for quantum information processing or for test of Bell's inequalities.Comment: 10 pages, 3 figures, published versio

Experimental Demonstration of Blind Quantum Computing

Quantum computers, besides offering substantial computational speedups, are also expected to provide the possibility of preserving the privacy of a computation. Here we show the first such experimental demonstration of blind quantum computation where the input, computation, and output all remain unknown to the computer. We exploit the conceptual framework of measurement-based quantum computation that enables a client to delegate a computation to a quantum server. We demonstrate various blind delegated computations, including one- and two-qubit gates and the Deutsch and Grover algorithms. Remarkably, the client only needs to be able to prepare and transmit individual photonic qubits. Our demonstration is crucial for future unconditionally secure quantum cloud computing and might become a key ingredient for real-life applications, especially when considering the challenges of making powerful quantum computers widely available

Atomistic Simulation for Transition Metal Dichalcogenides using NEMO5 and MedeA-VASP

This thesis is an attempt to understand and delve into the realm of atomistic simulations, using it to understand a novel set of materials called Transition Metal Dichalcogenides (TMDs). We use NEMO5 and MedeA-VASP to calibrate and characterize a few selected TMDs and to validate our understanding of atomistic modeling we simulated a tunnel field-effect transistor with monolayer TMD as a channel using NEMO5. TFETs offer great advantages over MOSFET (metal oxide field-effect devices) like, sub-60 mV/dec sub-threshold swing, minimal leakage current, high switching speed, and small power requirements. Low drive current has prevented TFETs from becoming a mainstream device instead of MOSFETs. Two methods of improving TFETs are being considered: one, making the device out of single-layered materials, and two, using different kinds of materials, TMDs being one of them. This research uses NEMO5 and MedeA-VASP atomistic modeling tools to understand both of the device improvement approaches mentioned above. Variation in parameters that matter at the atomic scale, like high symmetry k-point path, k-point meshing, and plane-wave cut-off energy exhibit prominent effects on the band-structure of a material. NEMO5 E-k band structures were simulated for TMDs like MoS2 and WTe2 and the band-gap structures obtained were compared with literature. Structure denition and atomistic device simulation were conducted in NEMO5. A TFET with a monolayer of MoS2 as a channel was simulated to see the I-V characteristics obtained from the NEMO5 tool. By performing electronic band-structure simulations with and without spin-orbit coupling (SOC) and comparing it against electronic structures presented in literature, it is shown that consideration of SOC is necessary for accurate results. Atomistic simulations are computationally intensive and this work also explored the effects of parametric and distributed computing settings on simulation times

Rigid Body Dynamics of Ship Hulls via Hydrostatic Forces Calculated From FFT Ocean Height Fields

An art tool is presented that utilizes a method for simulating the motion of ships in response to hydrostatic forces on the hull from a height-field representation of an ocean surface. Other forces modeled as a PID controller aid to steer the ship and stabilize the motion. The algorithms described can be applied to 3D models of arbitrary shapes composed of polygons floating on height fields generated from a myriad of additional spectra. The performance of the method is demonstrated in simple and complex ships, and ocean surfaces of at, medium, and large waveheights

Leveraging Analog Quantum Computing with Neutral Atoms for Solvent Configuration Prediction in Drug Discovery

We introduce quantum algorithms able to sample equilibrium water solvent molecules configurations within proteins thanks to analog quantum computing. To do so, we combine a quantum placement strategy to the 3D Reference Interaction Site Model (3D-RISM), an approach capable of predicting continuous solvent distributions. The intrinsic quantum nature of such coupling guarantees molecules not to be placed too close to each other, a constraint usually imposed by hand in classical approaches. We present first a full quantum adiabatic evolution model that uses a local Rydberg Hamiltonian to cast the general problem into an anti-ferromagnetic Ising model. Its solution, an NP-hard problem in classical computing, is embodied into a Rydberg atom array Quantum Processing Unit (QPU). Following a classical emulator implementation, a QPU portage allows to experimentally validate the algorithm performances on an actual quantum computer. As a perspective of use on next generation devices, we emulate a second hybrid quantum-classical version of the algorithm. Such a variational quantum approach (VQA) uses a classical Bayesian minimization routine to find the optimal laser parameters. Overall, these Quantum-3D-RISM (Q-3D-RISM) algorithms open a new route towards the application of analog quantum computing in molecular modelling and drug design

Optimization and evaluation of variability in the programming window of a flash cell with molecular metal-oxide storage

We report a modeling study of a conceptual nonvolatile memory cell based on inorganic molecular metal-oxide clusters as a storage media embedded in the gate dielectric of a MOSFET. For the purpose of this paper, we developed a multiscale simulation framework that enables the evaluation of variability in the programming window of a flash cell with sub-20-nm gate length. Furthermore, we studied the threshold voltage variability due to random dopant fluctuations and fluctuations in the distribution of the molecular clusters in the cell. The simulation framework and the general conclusions of our work are transferrable to flash cells based on alternative molecules used for a storage media

Can System Truncation Speed up Ligand-Binding Calculations with Periodic Free-Energy Simulations?

We have investigated whether alchemical free-energy perturbation calculations of relative binding energies can be sped up by simulating a truncated protein. Previous studies with spherical nonperiodic systems showed that the number of simulated atoms could be reduced by a factor of 26 without affecting the calculated binding free energies by more than 0.5 kJ/mol on average (Genheden, S.; Ryde, U. J. Chem. Theory Comput. 2012, 8, 1449), leading to a 63-fold decrease in the time consumption. However, such simulations are rather slow, owing to the need of a large cutoff radius for the nonbonded interactions. Periodic simulations with the electrostatics treated by Ewald summation are much faster. Therefore, we have investigated if a similar speed-up can be obtained also for periodic simulations. Unfortunately, our results show that it is harder to truncate periodic systems and that the truncation errors are larger for these systems. In particular, residues need to be removed from the calculations, which means that atoms have to be restrained to avoid that they move in an unrealistic manner. The results strongly depend on the strength on this restraint. For the binding of seven ligands to dihydrofolate reductase and ten inhibitors of blood-clotting factor Xa, the best results are obtained with a small restraining force constant. However, the truncation errors were still significant (e.g., 1.5-2.9 kJ/mol at a truncation radius of 10 Å). Moreover, the gain in computer time was only modest. On the other hand, if the snapshots are truncated after the MD simulations, the truncation errors are small (below 0.9 kJ/mol even for a truncation radius of 10 Å). This indicates that postprocessing with a more accurate energy function (e.g., with quantum chemistry) on truncated snapshots may be a viable approach

Experimentally Bounding Deviations From Quantum Theory in the Landscape of Generalized Probabilistic Theories

Many experiments in the field of quantum foundations seek to adjudicate between quantum theory and speculative alternatives to it. This requires one to analyze the experimental data in a manner that does not presume the correctness of the quantum formalism. The mathematical framework of generalized probabilistic theories (GPTs) provides a means of doing so. We present a scheme for determining which GPTs are consistent with a given set of experimental data. It proceeds by performing tomography on the preparations and measurements in a self-consistent manner, i.e., without presuming a prior characterization of either. We illustrate the scheme by analyzing experimental data for a large set of preparations and measurements on the polarization degree of freedom of a single photon. We first test various hypotheses for the dimension of the GPT vector space for this degree of freedom. Our analysis identifies the most plausible hypothesis to be dimension 4, which is the value predicted by quantum theory. Under this hypothesis, we can draw the following additional conclusions from our scheme: (i) that the smallest and largest GPT state spaces that could describe photon polarization are a pair of polytopes, each approximating the shape of the Bloch sphere and having a volume ratio of 0.977±0.001, which provides a quantitative bound on the scope for deviations from the state and effect spaces predicted by quantum theory, and (ii) that the maximal violation of the Clauser, Horne, Shimony, and Holt inequality can be at most 1.3%±0.1 greater than the maximum violation allowed by quantum theory, and the maximal violation of a particular inequality for universal noncontextuality can not differ from the quantum prediction by more than this factor on either side. The only possibility for a greater deviation from the quantum state and effect spaces or for greater degrees of supraquantum nonlocality or contextuality, according to our analysis, is if a future experiment (perhaps following the scheme developed here) discovers that additional dimensions of GPT vector space are required to describe photon polarization, in excess of the four dimensions predicted by quantum theory to be adequate to the task