Application Of Molecular Dynamics Research Articles

Generating Angular-Varying Time Delays of THz Pulses via Direct Space-to-Time Mapping of Metasurface Structures.

We experimentally demonstrate the generation of double terahertz (THz) pulses with tailored angular-dependent time delays from a nonlinear metasurface excited by a near-infrared femtosecond pulse. The tailored temporal properties of the generated pulses emerge from a direct mapping of the nonlinear spatial response of the metasurface to the emitted THz temporal profile. We utilize the Pancharatnam-Berry phase to implement symmetric and antisymmetric metasurface configurations and show that the emitted patterns present spatiotemporal "X-shaped" profiles after collimation by a parabolic mirror, with angular-dependent pulse delays corresponding to the intended design. In addition, we show that the addition of polarization multiplexing presents the opportunity to achieve a full range of elliptical THz polarizations. Double pulse generation and spatiotemporal shaping of THz waves in general show potential for THz spectroscopy and molecular dynamics applications, particularly in pump-probe experiments.

Review on Characterization of Biochar Derived from Biomass Pyrolysis via Reactive Molecular Dynamics Simulations

Biochar is a carbon-rich solid produced during the thermochemical processes of various biomass feedstocks. As a low-cost and environmentally friendly material, biochar has multiple significant advantages and potentials, and it can replace more expensive synthetic carbon materials for many applications in nanocomposites, energy storage, sensors, and biosensors. Due to biomass feedstock species, reactor types, operating conditions, and the interaction between different factors, the compositions, structure and function, and physicochemical properties of the biochar may vary greatly, traditional trial-and-error experimental approaches are time consuming, expensive, and sometimes impossible. Computer simulations, such as molecular dynamics (MD) simulations, are an alternative and powerful method for characterizing materials. Biomass pyrolysis is one of the most common processes to produce biochar. Since pyrolysis of decomposing biomass into biochar is based on the bond-order chemical reactions (the breakage and formation of bonds during carbonization reactions), an advanced reactive force field (ReaxFF)-based MD method is especially effective in simulating and/or analyzing the biomass pyrolysis process. This paper reviewed the fundamentals of the ReaxFF method and previous research on the characterization of biochar physicochemical properties and the biomass pyrolysis process via MD simulations based on ReaxFF. ReaxFF implicitly describes chemical bonds without requiring quantum mechanics calculations to disclose the complex reaction mechanisms at the nano/micro scale, thereby gaining insight into the carbonization reactions during the biomass pyrolysis process. The biomass pyrolysis and its carbonization reactions, including the reactivity of the major components of biomass, such as cellulose, lignin, and hemicellulose, were discussed. Potential applications of ReaxFF MD were also briefly discussed. MD simulations based on ReaxFF can be an effective method to understand the mechanisms of chemical reactions and to predict and/or improve the structure, functionality, and physicochemical properties of the products.

Application of molecular dynamics simulations in interface interaction of clay: Current status and perspectives

AbstractTo understand the research progress of molecular dynamics (MD) method in the field of clay minerals, the application of MD in the interface interaction of clay minerals is reviewed in this paper. MD simulations have become the indispensable means to study mineral interface effects. Clay minerals are common associated minerals with hydrophilic surface, the ease of argillization, negative electricity, and the ability of forming impurities and defects. They are widely concerned in the fields of mine wastewater treatment, fine clay mineral flotation, shale oil and gas exploitation, and so forth. In addition, clay minerals are considered as natural adsorbents due to their large specific surface area, but their complex interface interactions hinder their effective utilization. Therefore, it is particularly important to reveal the interaction mechanism of clay interface at the atomic/molecular level by means of software simulation technology. In this review, our focus is on the applications of MD method in the field of clay mineral interface interaction, such as clay/gas interface, clay/water interface, agents and clay/water interface, and mineral particle and clay/water interface. Furthermore, the history and shortcomings of MD simulation are summarized. The research and effective utilization of clay interface are summarized and prospected as well.

Ab initio real-time quantum dynamics of charge carriers in momentum space.

Application of the non-adiabatic molecular dynamics (NAMD) approach is limited to studying carrier dynamics in the momentum space, as a supercell is required to sample the phonon excitation and electron-phonon (e-ph) interaction at different momenta in a molecular dynamics simulation. Here we develop an ab initio approach for the real-time charge carrier quantum dynamics in the momentum space (NAMD_k) by directly introducing e-ph coupling into the Hamiltonian based on the harmonic approximation. The NAMD_k approach maintains the zero-point energy and includes memory effects of carrier dynamics. The application of NAMD_k to the hot carrier dynamics in graphene reveals the phonon-specific relaxation mechanism. An energy threshold of 0.2 eV-defined by two optical phonon modes-separates the hot electron relaxation into fast and slow regions with lifetimes of pico- and nanoseconds, respectively. The NAMD_k approach provides an effective tool to understand real-time carrier dynamics in the momentum space for different materials.

Research progress in molecular dynamics of high-performance PBO fibers

This article reviews the application and development of molecular dynamics in the field of poly(p-benzobisoxazole) (PBO) molecules, including the use of molecular dynamics simulations to calculate the theoretical Young’s modulus of PBO molecules and discuss them from the perspective of molecular theory Combine the rotational isomerism state theory with the long molecular dynamics simulation of small fragments to evaluate the limit length of the persistence vector a. The molecular dynamics calculation is used to study the molecular motion behavior of isolated rigid rod molecules such as PBO. Combining computer simulation technology and X-ray diffraction data collected by the imaging board system to analyze the crystal structure of the PBO fiber, and use molecular dynamics and dynamic modeling to establish the PBO/epoxy interface and study its performance.

Inhibitory effect of acarbose on tyrosinase: application of molecular dynamics integrating inhibition kinetics

Due to its clinical and cosmetic applications, investigators have paid attention to tyrosinase (TYR) inhibitor development. In this study, a TYR inhibition study with acarbose was investigated to gain insights into the regulation of the catalytic function. Biochemical assay results indicated that acarbose was turned to be an inhibitor of TYR in a reversible binding manner and probed as a distinctive mixed-type inhibitor via measurement of double-reciprocal kinetic (K i = 18.70 ± 4.12 mM). Time-interval kinetic measurement indicated that TYR catalytic function was gradually inactivated by acarbose in a time-dependent behavior displaying with a monophase process that was evaluated by semi-logarithmic plotting. Spectrofluorimetric measurement by integrating with a hydrophobic residue detector (1-anilinonaphthalene-8-sulfonate) showed that the high dose of acarbose derived a conspicuous local structural deformation of the TYR catalytic site pocket. Computational docking simulation showed that acarbose bound to key residues such as HIS61, TYR65, ASN81, HIS244, and HIS259. Our study extends an understanding of the functional application of acarbose and proposes that acarbose is an alternative candidate drug for a whitening agent via direct retardation of TYR catalytic function and it would be applicable for the relevant skin hyperpigmentation disorders concerning the dermatologic clinical purpose. Communicated by Ramaswamy H. Sarma

Application of Mixed-Solvent Molecular Dynamics Simulations for Prediction of Allosteric Sites on G Protein-Coupled Receptors.

The development of small molecule allosteric modulators acting at G protein-coupled receptors (GPCRs) is becoming increasingly attractive. Such compounds have advantages over traditional drugs acting at orthosteric sites on these receptors, in particular target specificity. However, the number and locations of druggable allosteric sites within most clinically relevant GPCRs are unknown. In the present study, we describe the development and application of a mixed-solvent molecular dynamics (MixMD)-based method for the identification of allosteric sites on GPCRs. The method employs small organic probes with druglike qualities to identify druggable hotspots in multiple replicate short-timescale simulations. As proof of principle, we first applied the method retrospectively to a test set of five GPCRs (cannabinoid receptor type 1, C-C chemokine receptor type 2, M2 muscarinic receptor, P2Y purinoceptor 1, and protease-activated receptor 2) with known allosteric sites in diverse locations. This resulted in the identification of the known allosteric sites on these receptors. We then applied the method to the μ-opioid receptor. Several allosteric modulators for this receptor are known, although the binding sites for these modulators are not known. The MixMD-based method revealed several potential allosteric sites on the mu-opioid receptor. Implementation of the MixMD-based method should aid future efforts in the structure-based drug design of drugs targeting allosteric sites on GPCRs. SIGNIFICANCE STATEMENT: Allosteric modulation of G protein-coupled receptors (GPCRs) has the potential to provide more selective drugs. However, there are limited structures of GPCRs bound to allosteric modulators, and obtaining such structures is problematic. Current computational methods utilize static structures and therefore may not identify hidden or cryptic sites. Here we describe the use of small organic probes and molecular dynamics to identify druggable allosteric hotspots on GPCRs. The results reinforce the importance of protein dynamics in allosteric site identification.

Molecular dynamic studies into the comparative optimization of thermo-mechanical characters of nano-composites of Ag and Cu reinforced by Graphene.

This article fundamentally aims at the comparative study of thermo-mechanical characters of Gr/Ag and Gr/Cu nano-composites. For demonstration purposes, three dimensions that is, (1 0 0), (1 1 0) and (1 1 1), of the metals attached with single layer Graphene sheet are considered. The study is facilitated by the adaptation of the molecular dynamic simulations of the soft LAMMPS to mimic the broad range of experimental environment. The attributes of each structure and their orientations are elaborated over wide range of experimental states, encompassing temperature ranging from 300 K to 1500 K, to assess the melting behavior. The thermal and structural properties are explored by employing mean square displacement (MSD) and radial distribution function (RDF). Furthermore, the mechanical characters are elaborated along both arm-chair and zigzag directions. The findings are supported by producing relevant graphical displays of stress-strain curves and generating extravagant depictions of various dislocations with the application of visual molecular dynamics (VMD) tool. On the basis of intense and careful computational investigations, we witnessed that the Gr/Cu (1 1 1) orientation produced most profound melting characteristics along with distinctive strengthening and fracture mechanism. These outcomes are consistent in comparison of both Gr/Metals layered structures and also with respect to all considered metallic orientations. The findings are discussed thoroughly in a well-structured and synchronized fashion throughout the article.

Structure-based virtual screening of novel natural products as chalcone derivatives against SARS-CoV-2 Mpro

Coronavirus disease 2019 (COVID-19), which is caused by SARS-CoV-2, has spread quickly around the world, causing a global pandemic. It has infected more than 500 million people as of April 28, 2022. Much research has been reported to stop the virus from spreading, but there are currently no approved medicines to treat COVID-19. In this work, a dataset of 142 natural products collected from various medicinal plants was used to perform structure-based virtual screening (SBVS) through the combined application of molecular docking and molecular dynamics (MD) simulation methods. First, the dataset of compounds was optimized using the density functional theory (DFT) approach. The optimized compounds were then submitted to the first screening, which was done by the pKCM web server to look for drug-likeness and the PyRx to look for binding affinity. Among the 142 natural substances, 10 compounds were selected for docking validation. Compounds that interact with CYS145 and LEU141, the essential catalytic residues, as well as compounds with binding affinities less than −8.0 kcal/mol, are considered promising anti-SARS-CoV-2 drug candidates. The top-ranked compounds were then evaluated by MD simulations and MM-GBSA method. These results could help researchers come up with new natural compounds that could be used to treat SARS-CoV-2. Communicated by Ramaswamy H. Sarma

Application of molecular dynamics to elucidate key binding interactions for the development of therapeutics against opioid overdose.

Opioid overdose has been a long-standing public health issue in the United States. This crisis has only been exacerbated by the Covid-19 pandemic, with overdose deaths involving opioids increasing from an estimated 70,029 in 2020 to 80,816 in 2021. While there are treatments for opioid overdose, there are currently no therapeutic tools to prevent it. Moreover, these treatments are limited to emergency scenarios, most notably due to induction of withdrawal and loss of analgesia. Fatal opioid overdoses are primarily attributed to opioid-induced respiratory depression (OIRD). As part of an ongoing collaboration, a class of cysteine esters have been identified that reverse OIRD without blocking the analgesic effects of the opioid or inducing withdrawal. Our working hypothesis is that these esters function by binding β-arrestin and altering either its interaction with the opioid receptor, downstream proteins, or both. Accordingly, we have used “flooding” molecular dynamics simulations to identify candidate binding sites for several related ligands on the surface of β-arrestin 1 and 2, which we then validate using alchemical ligand binding free energy calculations. The results will be used to suggest mutations that would disrupt binding and to better understand the mechanism by which these compounds combat opioid overdose.

Molecular Dynamics Simulation Studies of Properties, Preparation, and Performance of Silicon Carbide Materials: A Review

Silicon carbide (SiC) materials are widely applied in the field of nuclear materials and semiconductor materials due to their excellent radiation resistance, thermal conductivity, oxidation resistance, and mechanical strength. The molecular dynamics (MD) simulation is an important method to study the properties, preparation, and performance of SiC materials. It has significant advantages at the atomic scale. The common potential functions for MD simulations of silicon carbide materials were summarized firstly based on extensive literatures. The key parameters, complexity, and application scope were compared and analyzed. Then, the MD simulation of SiC properties, preparation, and performance was comprehensively overviewed. The current studies of MD simulation methods and applications of SiC materials were systematically summarized. It was found that the Tersoff potential was the most widely applied potential function for the MD simulation of SiC materials. The construction of more accurate potential functions for special application fields was an important development trend of potential functions. In the MD simulation of SiC properties, the thermal properties and mechanical properties, including thermal conductivity, hardness, elastic modulus, etc., were mainly studied. The correlation between MD simulations of microscopic processes and the properties of macroscopic materials, as well as the methods for obtaining different property parameters, were summarized. In the MD simulation of SiC preparation, ion implantation, polishing, sputtering, deposition, crystal growth, amorphization, etc., were mainly studied. The chemical vapor deposition (CVD) and sintering methods commonly applied in the preparation of SiC nuclear materials were reported rarely and needed to be further studied. In the MD simulation of SiC performance, most of the present studies were related to SiC applications in the nuclear energy research. The irradiation damage simulation in the field of nuclear materials was studied most widely. It can be found that SiC materials in the field of nuclear materials study were a very important topic. Finally, the future perspective of MD simulation studies of SiC materials were given, and development suggestions were summarized. This paper is helpful for understanding and mastering the general method of computation material science aimed at the multi-level analysis. It also has a good reference value in the field of SiC material study and MD method study.

Molecular Dynamics (MD) Applications in Materials Science and Engineering and Nanotechnology

Molecular Dynamics (MD) Applications in Materials Science and Engineering and Nanotechnology

Mass transfer of multi-pollutants over titania-based SCR catalyst: A molecular dynamics study

Mass transfer can significantly affect the SCR process which is designed for NOx removal. However, it is still challenging to characterize the transport of gaseous species involved in the process, especially at nano-scale. This work probes into the application of non-equilibrium molecular dynamics (NEMD) simulations to study the mass transfer of multi-pollutants over a titania-based catalyst. A dual control-volume (DCV) model was proposed to simulate transport of typical gaseous molecules (e.g. NO, NH3 and SO2). The impacts of temperature, pore width, hydroxyl sites and competitive diffusion on diffusivity of objective molecules were studied in details. The results showed that temperature and surface sites could affect NH3 more significantly than NO and SO2, yet the influence of surface sites was strongly size-dependent. The reduction in NH3 diffusivity caused by the presence of surface sites decreased from 32.37 % to 2.97 % when the pore width grows from 25 Å to 75 Å. The competitive transport between NH3 and SO2 has also mitigated the impacts of surface sites on both molecules.

The role of water at electrified metal-water interfaces unravelled from first principles

Electrified metal-water interfaces are a key feature in many devices and processes, finding applications in a variety of fields, including corrosion, photo/electrocatalysis, and energy. For over 200 years after Faraday established his ground-breaking law, electrochemistry has been subject to intense research, due to its broad applications and interdisciplinary nature. However, it remains an open challenge to provide a comprehensive description of molecular scale structure and processes at electrified interfaces in electrochemical conditions. In this review, we highlight the most recent advancements in the application of ab initio molecular dynamics (AIMD) to study metal-water interfaces, noting how this work aligns with experimental and other theoretical models. We show how AIMD simulations have unveiled new perspectives on the crucial impact of water on determining surface potentials, the chemistry of surface adsorbates, and capacitive response under electrochemical conditions. We highlight how this work aligns with experimental and other simplified theoretical models.

Application of Molecular Dynamics to Expand Docking Program's Exploratory Capabilities and to Evaluate Its Predictions.

Recognition of the growing importance of RNA as a target for therapeutic or diagnostic ligands brings the importance of computational predictions of docking poses to such receptors to the forefront. Most docking programs have been optimized for protein targets, based on a relatively rich pool of known docked protein structures. Unfortunately, despite progress, numbers of known docked RNA complexes are low and the accuracy of the computational predictions trained on those inadequate samples lags behind that achieved for proteins. Compared to proteins, RNA structures generally have fewer docking pockets, have less diverse electrostatic surfaces, and are more flexible, raising the possibility of producing only transiently available good docking targets. We are presenting a docking prediction protocol that adds molecular dynamics simulations before and after the actual docking in order to explore the conformational space of the target RNA and then to reevaluate the stability of the predicted RNA-ligand complex. In this way we are attempting to overcome important limitations of the docking programs: the rigid (fully or mostly) target structure and imperfect nature of the docking scoring functions.

Temperature-dependent multiscale modeling of graphene sheet under finite deformation

The homogenized constitutive models that have been utilized to simulate the behavior of nanostructures are typically based on the Cauchy–Born hypothesis, which seeks the fundamental properties of material via relating atomistic information to an assumed homogeneous deformation field. It is well known that temperature has a profound effect on the validity and size-dependency of the Cauchy-Born hypothesis in finite deformations. In this study, a temperature-related Cauchy–Born formulation is established for graphene sheets and its performance is examined through a direct comparison between the continuum-based constitutive model and molecular dynamics analysis. It is demonstrated that if the temperature increases, the validity surfaces shrink, which is not highly dependent on the size of specimen. At finite strains, graphene sheet exhibits material softening and hardening, which are manifested in the elastic constants. The developed constitutive model is used to study the effect of applied deformations at various temperature levels on the elastic constants of graphene sheets. Finally, a novel multiscale finite element approach is developed for the analysis of graphene sheets in finite strain regime based on the proposed atomistic-continuum model. The method can be used efficiently in the simulation of large specimens where the application of molecular dynamics requires considerable computational efforts. The efficiency and robustness of the proposed multiscale approach are shown through several numerical examples.

Path-integral molecular dynamics for anyons, bosons, and fermions.

In this article we develop a general method to numerically calculate physical properties for a system of anyons with path integral molecular dynamics. We provide a unified method to calculate the thermodynamics of identical bosons, fermions, and anyons. Our method is tested and applied to systems of anyons, bosons, and fermions in a two-dimensional harmonic trap. We also consider a method to calculate the energy for fermions as an application of the path integral molecular dynamics to simulate the anyon model.

Transferable and Polarizable Coarse Grained Model for Proteins─ProMPT.

The application of classical molecular dynamics (MD) simulations at atomic resolution (fine-grained level, FG), to most biomolecular processes, remains limited because of the associated computational complexity of representing all the atoms. This problem is magnified in the presence of protein-based biomolecular systems that have a very large conformational space, and MD simulations with fine-grained resolution have slow dynamics to explore this space. Current transferable coarse grained (CG) force fields in literature are either limited to only peptides with the environment encoded in an implicit form or cannot capture transitions into secondary/tertiary peptide structures from a primary sequence of amino acids. In this work, we present a transferable CG force field with an explicit representation of the environment for accurate simulations with proteins. The force field consists of a set of pseudoatoms representing different chemical groups that can be joined/associated together to create different biomolecular systems. This preserves the transferability of the force field to multiple environments and simulation conditions. We have added electronic polarization that can respond to environmental heterogeneity/fluctuations and couple it to protein's structural transitions. The nonbonded interactions are parametrized with physics-based features such as solvation and partitioning free energies determined by thermodynamic calculations and matched with experiments and/or atomistic simulations. The bonded potentials are inferred from corresponding distributions in nonredundant protein structure databases. We present validations of the CG model with simulations of well-studied aqueous protein systems with specific protein fold types─Trp-cage, Trpzip4, villin, WW-domain, and β-α-β. We also explore the applications of the force field to study aqueous aggregation of Aβ 16-22 peptides.

The 70-year search for the voltage-sensing mechanism of ion channels.

This retrospective on the voltage‐sensing mechanisms and gating models of ion channels begins in 1952 with the charged gating particles postulated by Hodgkin and Huxley, viewed as charges moving across the membrane and controlling its permeability to Na+ and K+ ions. Hodgkin and Huxley postulated that their movement should generate small and fast capacitive currents, which were recorded 20 years later as gating currents. In the early 1980s, several voltage‐dependent channels were cloned and found to share a common architecture: four homologous domains or subunits, each displaying six transmembrane α‐helical segments, with the fourth segment (S4) displaying four to seven positive charges invariably separated by two non‐charged residues. This immediately suggested that this segment was serving as the voltage sensor of the channel (the molecular counterpart of the charged gating particle postulated by Hodgkin and Huxley) and led to the development of the sliding helix model. Twenty years later, the X‐ray crystallographic structures of many voltage‐dependent channels allowed investigation of their gating by molecular dynamics. Further understanding of how channels gate will benefit greatly from the acquisition of high‐resolution structures of each of their relevant functional or structural states. This will allow the application of molecular dynamics and other approaches. It will also be key to investigate the energetics of channel gating, permitting an understanding of the physical and molecular determinants of gating. The use of multiscale hierarchical approaches might finally prove to be a rewarding strategy to overcome the limits of the various single approaches to the study of channel gating.

Molecular dynamics application of cocrystal energetic materials: A review

Abstract Cocrystallization is an important method to obtain high-energy and low-sensitivity explosives. Therefore, the synthesis, structures, and properties of cocrystal energetic materials have become a highly active research topic. Studying the physical and chemical properties of cocrystal energetic materials by molecular dynamics is of great significance for the in-depth understanding and design/synthesis of new cocrystal energetic materials. This review introduces the method of molecular dynamics, the cocrystal energetic materials synthesized successfully to date, and the application of molecular dynamics to cocrystal energetic materials. The existing problems and future development directions are discussed. We hope that this review will encourage researchers interested in the field to design and synthesize high-energy and low-sensitive energetic materials with practical application value.