Parallel Tempering Monte Carlo Simulations Research Articles

Simulation Study of Polyethylene Terephthalate Hydrolase Adsorption on Self-Assembled Monolayers.

Polyethylene terephthalate (PET) hydrolase, discovered in Ideonella sakaiensis (IsPETase), is a promising agent for the biodegradation of PET under mild reaction conditions, yet the thermal stability is poor. The efficient immobilization and orientation of IsPETase on different solid substrates are essential for its application. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of IsPETase adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (SCDs). The results show that the protein adsorption orientation was determined not only by attraction interactions but also by repulsion interactions. IsPETase is adsorbed on the COOH-SAM surface with an "end-on" orientation, which favors the exposure of the catalyzed triplet to the solution. In addition, the entrance to the catalytic active center is larger on the COOH-SAM surface with a low SCD. This work reveals the controlled orientation and conformational information on IsPETase on charged surfaces at the atomistic level. This study would certainly promote our understanding of the mechanism of IsPETase adsorption and provide theoretical support for the design of substrates for IsPETase immobilization.

Structure and Thermodynamics of Li+Arn Clusters beyond the Second Solvation Shell

Small Li+Arn clusters are employed in this work as model systems to study microsolvation. Although first and second solvation shells are expected to be the most relevant ones for this type of atomic solvents, it is also interesting to explore larger clusters in order to identify the influence of external atoms on structural and thermodynamic properties. In this work, we perform a global geometry optimization for Li+Arn clusters (with n = 41–100) and parallel tempering Monte Carlo (PTMC) simulations for some selected sizes. The results show that global minimum structures of large clusters always have 6 argon atoms in the first solvation shell while maintaining the number of 14 or 16 argon atoms in the second one. By contrast, third and fourth solvation shells vary significantly the number of argon atoms with the cluster size, and other shells can hardly be assigned due to the reduced influence of Li+ on the external argon atoms for large clusters. In turn, PTMC calculations show that the melting of the most external solvation shells of large microsolvation clusters occurs at T∼50K, which is independent of cluster size. Structural transitions can be observed between quasi-degenerated structures at low temperatures. Moreover, the present results highlight the fluxional character of the external solvation shells of these large Li+Arn clusters, which may be seen as typical “snowball” structures.

Efficiently Differentiating Agonists and Competitive Antagonists for Weak Allosteric Protein-Ligand Interactions with Linear Response Theory.

What makes an agonist and a competitive antagonist? In this work, we aim to answer this question by performing parallel tempering Monte Carlo simulations on the serotonin type 3A (5-HT3A) receptor. We use linear response theory to predict conformational changes in the 5-HT3A receptor active site after weak perturbations are applied to its allosteric binding sites. A covariance tensor is built from conformational sampling of its apo state, and a harmonic approximation allows us to substitute the calculation of ligand-induced forces with the binding site's displacement vector. Remarkably, our study demonstrates the feasibility of effectively discerning between agonists and competitive antagonists for multiple ligands, requiring computationally expensive calculations only once per protein.

Simulation insights into the lipase adsorption on zeolitic imidazolate framework-8

Zeolitic imidazolate frameworks (ZIFs) have recently emerged as immobilization matrices for biomolecules, most notably enzymes. Understanding the key factors that dominate the enzyme's catalytic activity on/in ZIFs is crucial for the development of new immobilization matrices. In this work, a combination of the parallel tempering Monte Carlo simulation and all-atom molecular dynamics simulation is performed to study the orientation and conformation of the Candida rugose lipase (CRL) adsorbed on oppositely charged and neutral ZIF-8 (i.e., ZIF-8-COOH, ZIF-8-NH2, and ZIF-8-neutral) surfaces. The results show that CRL could adsorb on all ZIF-8 surfaces, with an ordered orientation obtained on charged ZIF-8 surfaces. ZIF-8-NH2 is a good candidate for CRL immobilization since it can maximize the catalytic activity of CRL. The native conformation of CRL is well preserved on all three surfaces due to the partially water-containing surface of ZIF-8. The results could provide theoretical support for the application of porous materials in enzyme immobilization.

Finite-temperature stability of hydrocarbons: Fullerenes vs flakes

The effects of a finite temperature on the equilibrium structures of hydrocarbon molecules are computationally explored as a function of size and relative chemical composition in hydrogen and carbon. Using parallel tempering Monte Carlo simulations employing a reactive force field, we find that in addition to the phases already known for pure carbon, namely, cages, flakes, rings, and branched structures, strong changes due to temperature and the addition of little amounts of hydrogen are reported. Both entropy and the addition of moderate amounts of hydrogen favor planar structures such as nanoribbons over fullerenes. Accurate phase diagrams are proposed, highlighting the possible presence of multiple phase changes at finite size and composition. Astrophysical implications are also discussed.

Molecular Simulation of Statherin Adsorption on Hydroxyapatite (001) Surface

AbstractStatherin (SN) is an important protein that can adsorb on enamel to maintain calcium ions balance and promote biomineralization in the human oral cavity. In this work, parallel tempering Monte Carlo simulation and all‐atom molecular dynamics simulation are combined to study the behavior of SN adsorbed on the hydroxyapatite (HAP) (001) surface. The results indicate that SN can “anchor” on HAP (001) surface by its Asp1 and Sep2 with “head‐on” orientation in NaCl solution and its secondary structure and conformation are changed greatly, which means that SN loses its biological activity. However, SN can maintain its conformation in calcium phosphate solution. Furthermore, SN can adsorb on HAP (001) surface with Sep2 and Sep3 by salt bridge with calcium phosphorus clusters with “lying” orientation. More importantly, Glu26 residue can stabilize the free calcium and phosphorus clusters, which can prevent not only the dissolution of HAP surface, but also the precipitation of calcium phosphate due to the supersaturated state. This work can help to better understand the process of biomineralization and also provides a guidance for the design of dental restoration materials.

Magnetic frustration in the cubic double perovskite Ba2NiIrO6

Hybrid transition metal oxides continue to attract attention due to their multiple degrees of freedom ($e.g.$, lattice, charge, spin, and orbital) and versatile properties. Here we investigate the magnetic and electronic properties of the newly synthesized double perovskite Ba$_2$NiIrO$_6$, using crystal field theory, superexchange model analysis, density functional calculations, and parallel tempering Monte Carlo (PTMC) simulations. Our results indicate that Ba$_2$NiIrO$_6$ has the Ni$^{2+}$ ($t_{2g}^{6}e_{g}^{2}$)-Ir$^{6+}$ ($t_{2g}^{3}$) charge states. The first nearest-neighboring (1NN) Ni$^{2+}$-Ir$^{6+}$ ions prefer a ferromagnetic (FM) coupling as expected from the Goodenough-Kanamori-Anderson rules, which contradicts the experimental antiferromagnetic (AF) order in Ba$_2$NiIrO$_6$. We find that the strong 2NN AF couplings are frustrated in the fcc sublattices, and they play a major role in determining the observed AF ground state. We also prove that the $J_{\rm eff}$ = 3/2 and $J_{\rm eff}$ = 1/2 states induced by spin-orbit coupling, which would be manifested in low-dimensional (e.g., layered) iridates, are however not the case for cubic Ba$_2$NiIrO$_6$. Our PTMC simulations show that when the long-range (2NN and 3NN) AF interactions are included, an AF transition with $T_{\rm N}$ = 66 K would be obtained and it is well comparable with the experimental 51 K. Meanwhile, we propose a possible 2$\times$2$\times$2 noncollinear AF structure for Ba$_2$NiIrO$_6$.

Thermodynamic Signatures of Structural Transitions and Dissociation of Charged Colloidal Clusters: A Parallel Tempering Monte Carlo Study.

Computational simulation of colloidal systems make use of empirical interaction potentials that are founded in well-established theory. In this work, we have performed parallel tempering Monte Carlo (PTMC) simulations to calculate heat capacity and to assess structural transitions, which may occur in charged colloidal clusters whose effective interactions are described by a sum of pair potentials with attractive short-range and repulsive long-range components. Previous studies on these systems have shown that the global minimum structure varies from spherical-type shapes for small-size clusters to Bernal spiral and “beaded-necklace” shapes at intermediate and larger sizes, respectively. In order to study both structural transitions and dissociation, we have organized the structures appearing in the PTMC calculations by three sets according to their energy: (i) low-energy structures, including the global minimum; (ii) intermediate-energy “beaded-necklace” motifs; (iii) high-energy linear and branched structures that characterize the dissociative clusters. We observe that, depending on the cluster, either peaks or shoulders on the heat–capacity curve constitute thermodynamics signatures of dissociation and structural transitions. The dissociation occurs at for all studied clusters and it is characterized by the appearance of a significant number of linear structures, while the structural transitions corresponding to unrolling the Bernal spiral are quite dependent on the size of the colloidal system.

Stability of skyrmion crystal phase in antiferromagnetic triangular lattice with DMI and single-ion anisotropy

We study a frustrated antiferromagnetic Heisenberg model on a triangular lattice with the Dzyaloshinskii–Moriya interaction (DMI) in the presence of an external magnetic field and focus on the effects of the single-ion anisotropy on the overall phase diagram topology and the skyrmion lattice (SkX) phase stability. Phase diagrams in the temperature-field plane for both easy-axis and easy-plane anisotropy of a varying strength are constructed in the regimes of a moderate and strong DMI by parallel tempering Monte Carlo simulations. For the considered range of parameters the phase diagrams featuring up to four ordered phases are identified. The SkX phase is found to be stabilized within some temperature and field window for sufficiently large DMI and not too strong anisotropy. We demonstrate that both types of the anisotropy can have beneficial effects on the SkX phase stabilization. Namely, in the systems with moderate DMI a small easy-plane anisotropy extends the field window of the SkX phase appearance by shifting its lower bound to smaller values and in the systems with larger DMI a small easy-axis anisotropy shifts the entire field range of the SkX phase stabilization towards smaller values. The Metropolis dynamics is employed to probe the persistence of the SkX phase upon quenching the field to zero or small finite values. It is confirmed that low temperatures, small DMI and small easy-plane anisotropy values support the skyrmions persistence, i.e., increase their lifetime.

Spirals and skyrmions in antiferromagnetic triangular lattices

We study realizations of spirals and skyrmions in two-dimensional antiferromagnets with a triangular lattice on an inversion-symmetry-breaking substrate. As a possible material realization, we investigate the adsorption of transition-metal atoms (Cr, Mn, Fe, or Co) on a monolayer of MoS$_2$, WS$_2$, or WSe$_2$ and obtain the exchange, anisotropy, and Dzyaloshinskii-Moriya interaction parameters using first-principles calculations. Using energy minimization and parallel-tempering Monte-Carlo simulations, we determine the magnetic phase diagrams for a wide range of interaction parameters. We find that skyrmion lattices can appear even with weak Dzyaloshinskii-Moriya interactions, but their stability is hindered by magnetic anisotropy. However, a weak easy plane magnetic anisotropy can be beneficial for stabilizing the skyrmion phase. Our results suggest that Cr$/$MoS$_2$, Fe$/$MoS$_2$, and Fe$/$WSe$_2$ interfaces can host spin spirals formed from the 120$^{\circ}$ antiferromagnetic states. Our results further suggests that for other interfaces, such as Fe$/$MoS$_2$, the Dzyaloshinskii-Moriya interaction is strong enough to drive the system into a three-sublattice skyrmion lattice in the presence of experimentally feasible external magnetic field.

Melting of Fe-terephthalate layers on Cu(1 0 0) surface with randomly distributed point defects

In this theoretical work, we study the influence of the concentration and type of randomly distributed point defects on crystalline solid surfaces on the possibility of self-assembly and thermal stability of surface confined metal-organic networks (SMON). As an example, we chose fundamentally different and well-studied SMONs of Fe-terephthalate on Cu(100) surface: cloverleaf and single-row structures. Using parallel tempering Monte Carlo simulation, we have determined the concentration thresholds for various types of defects above which the SMONs self-assembly is unfavorable. It is shown that the SMONs melting temperatures decrease equally with an increase in the surface concentration of point defects, regardless of the SMON type. Maximum decrease in the SMON melting temperature relative to the homogeneous surface reaches 15–23%, depending on the defect type. Melting of a more “rigid” single-row structure formed only by the coordination bonds is found to occur through the first-order phase transition, while the cloverleaf structure, stabilized mainly by weak hydrogen bonds and long-range substrate mediated interactions, is a continuous phase transition.

Emergent Potts order in the kagome J1−J3 Heisenberg model

Motivated by the physical properties of Vesignieite BaCu$_3$V$_2$O$_8$(OH)$_2$, we study the $J_1-J_3$ Heisenberg model on the kagom\'e lattice, that is proposed to describe this compound for $J_1<0$ and $J_3\gg|J_1|$. The nature of the classical ground state and the possible phase transitions are investigated through analytical calculations and parallel tempering Monte Carlo simulations. For $J_1<0$ and $J_3>\frac{1+\sqrt{5}}4|J_1|$, the ground states are not all related by an Hamiltonian symmetry. Order appears at low temperature via the order by disorder mechanism, favoring colinear configurations and leading to an emergent $q=4$ Potts parameter. This gives rise to a finite temperature phase transition. Effect of quantum fluctuations are studied through linear spin wave approximation and high temperature expansions of the $S=1/2$ model. For $J_3$ between $\frac14|J_1|$ and $\frac{1+\sqrt{5}}4|J_1|$, the ground state goes through a succession of semi-spiral states, possibly giving rise to multiple phase transitions at low temperatures.

First-principles melting of krypton and xenon based on many-body relativistic coupled-cluster interaction potentials

The solid-to-liquid phase transition for krypton and xenon is studied by means of parallel-tempering Monte Carlo simulations based on an accurate description of the atomic interactions within a many-body ansatz using relativistic coupled-cluster theory. These high-level data were subsequently fitted to computationally efficient extended Lennard-Jones and extended Axilrod-Teller-Muto types of interaction potentials. Solid-state calculations demonstrate that the many-body decomposition of the interaction energy converges well for the heavier rare gas solids, leading to solid-state properties in good agreement with experiment. The results show that it suffices to include two- and three-body interactions only for the melting simulation. The melting of the bulk is simulated for cells with cubic periodic boundary conditions, as well as within a finite cluster approach. For the latter, melting of spherical magic number clusters with increasing cluster size is studied, and the melting temperatures are obtained from extrapolation to the bulk. The calculated melting temperatures for the cluster extrapolation (the periodic approach values corrected for superheating are set in parentheses) are ${T}_{m}=113.7$ K (110.9 K) and ${T}_{m}=160.8$ K (156.1 K) for krypton and xenon, respectively. Both are in very good agreement with corresponding experimental values of 115.75 and 161.40 K.

A thermodynamic view on the microsolvation of ions by rare gas: application to Li+ with argon.

We present a thermodynamic perspective of the microsolvation of ions by rare gas atoms, which is based on parallel tempering Monte Carlo (PTMC) simulations. This allows the establishment of a clear relationship between the structure of the solvation shells and the heat capacity (CV) as a function of the number of individual solvent species. The dependence of CV on the temperature allows the identification of the internal structure rearrangements and the onset of partial or total melting of the clusters. As an application, we have employed the PTMC technique to study the thermodynamic properties of clusters resulting from the microsolvation of Li+ by argon atoms. Specifically, calculations have been carried out for the clusters Li+Arn (n = 4-18, 33, 34, and 38) by applying two different potential energy surfaces (PESs): one includes only two-body interactions, while the other also incorporates three-body contributions. Whenever possible, we compare the present thermodynamic results with global optimization studies carried out previously (F. V. Prudente, J. M. C. Marques and F. B. Pereira, Phys. Chem. Chem. Phys., 2017, 19, 25707; W. S. Jesus et al., Int. J. Quantum Chem., 2019, 119, e25860). We conclude that the melting process arises for lower temperatures when the model PES accounts for three-body interactions. Additionally, we characterize the melting processes of the first and second solvation shells. For some specific clusters, structural rearrangements of the most external argon atoms are observed at very low temperatures.

Simulated revelation of the adsorption behaviours of acetylcholinesterase on charged self-assembled monolayers.

An acetylcholinesterase (AChE)-based electrochemical biosensor, as a promising alternative to detect organophosphates (OPs) and carbamate pesticides, has gained considerable attention in recent years, due to the advantages of simplicity, rapidity, reliability and low cost. The bio-activity of AChE immobilized on the surface and the direct electron transfer (DET) rate between an enzyme and an electrode directly determined the analytical performances of the AChE-based biosensor, and experimental studies have shown that the charged surfaces have a strong impact on the detectability of the AChE-based biosensor. Therefore, it is very important to reveal the behaviour of AChE in bulk solution and on charged surfaces at the molecular level. In this work, the adsorption orientation and conformation of AChE from Torpedo californica (TcAChE) on oppositely charged self-assembled monolayers (SAMs), COOH-SAM and NH2-SAM with different surface charge densities, were investigated by parallel tempering Monte Carlo (PTMC) and all-atom molecular dynamics simulations (AAMD). Simulation results show that TcAChE could spontaneously and stably adsorb on two oppositely charged surfaces by the synergy of an electric dipole and charged residue patch, and opposite orientations were observed. The active-site gorge of TcAChE is oriented toward the surface with the "end-on" orientation and the active sites are close to the surface when it is adsorbed on the positively charged surface and the tunnel cost for the substrate is lower than that on the negatively charged surface and in bulk solution, while for TcAChE adsorbed on the negatively charged surface, the active site of TcAChE is far away from the surface and the active-site gorge is oriented toward the solution with a "back-on" orientation. It suggests that the positively charged surface could provide a better microenvironment for the efficient bio-catalytic reaction and quick DET between TcAChE and the electrode surface. Moreover, the RMSD, RMSF, dipole moment, gyration radius, eccentricity and superimposed structures show that only a slight conformational change occurred on the relatively flexible structure of TcAChE during simulations, and the native conformation is well preserved after adsorption. This work helps us better comprehend the adsorption mechanism of TcAChE on charged surfaces and might provide some guidelines for the development of new TcAChE-based amperometric biosensors for the detection of organophosphorus pesticides.

Parallel Tempering Monte Carlo Studies of Phase Transition of Free Boundary Planar Surfaces.

We numerically study surface models defined on hexagonal disks with a free boundary. 2D surface models for planar surfaces have recently attracted interest due to the engineering applications of functional materials such as graphene and its composite with polymers. These 2D composite meta-materials are strongly influenced by external stimuli such as thermal fluctuations if they are sufficiently thin. For this reason, it is very interesting to study the shape stability/instability of thin 2D materials against thermal fluctuations. In this paper, we study three types of surface models including Landau-Ginzburg (LG) and Helfirch-Polyakov models defined on triangulated hexagonal disks using the parallel tempering Monte Carlo simulation technique. We find that the planar surfaces undergo a first-order transition between the smooth and crumpled phases in the LG model and continuous transitions in the other two models. The first-order transition is relatively weak compared to the transition on spherical surfaces already reported. The continuous nature of the transition is consistent with the reported results, although the transitions are stronger than that of the reported ones.

Phase diagram of dipolar-coupled XY moments on disordered square lattices

The effects of dilution disorder and random-displacement disorder are analyzed for dipolar-coupled magnetic moments confined in a plane, which were originally placed on the square lattice. In order to distinguish the different phases, new order parameters are derived and parallel tempering Monte Carlo simulations are performed for a truncated dipolar Hamiltonian to obtain the phase diagrams for both types of disorder. We find that both dilution disorder and random-displacement disorder give similar phase diagrams, namely disorder at small enough temperatures favors a so-called microvortex phase. This can be understood in terms of the flux closure present in dipolar-coupled systems.

Bilirubin Oxidase Adsorption onto Charged Self-Assembled Monolayers: Insights from Multiscale Simulations.

The efficient immobilization and orientation of bilirubin oxidase (BOx) on different solid substrates are essential for its application in biotechnology. The T1 copper site within BOx is responsible for the electron transfer. In order to obtain quick direct electron transfer (DET), it is important to keep the distance between the T1 copper site and electrode surface small and to maintain the natural structure of BOx at the same time. In this work, the combined parallel tempering Monte Carlo simulation with the all-atom molecular dynamics simulation approach was adopted to reveal the adsorption mechanism, orientation, and conformational changes of BOx from Myrothecium verrucaria (MvBOx) adsorbed on charged self-assembled monolayers (SAMs), including COOH-SAM and NH2-SAM with different surface charge densities (±0.05 and ±0.19 C·m-2). The results show that MvBOx adsorbs on negatively charged surfaces with a "back-on" orientation, whereas on positively charged surfaces, MvBOx binds with a "lying-on" orientation. The locations of the T1 copper site are closer to negatively charged surfaces. Furthermore, for negatively charged surfaces, the T1 copper site prefers to orient closer to the surface with lower surface charge density. Therefore, the negatively charged surface with low surface charge density is more suitable for the DET of MvBOx on electrodes. Besides, the structural changes primarily take place on the relatively flexible turns, coils, and α-helix. The native structure of MvBOx is well preserved when it adsorbs on both charged surfaces. This work sheds light on the controlling orientation and conformational information on MvBOx on charged surfaces at the atomistic level. This understanding would certainly promote our understanding of the mechanism of MvBOx immobilization and provide theoretical support for BOx-based bioelectrode design.

A Hundred-Year-Old Experiment Re-evaluated: Accurate Ab Initio Monte Carlo Simulations of the Melting of Radon.

State-of-the-art relativistic coupled-cluster theory is used to construct many-body potentials for the noble-gas element radon to determine its bulk properties including the solid-to-liquid phase transition from parallel tempering Monte Carlo simulations through either direct sampling of the bulk or from a finite cluster approach. The calculated melting temperature are 200(3) K and 200(6) K from bulk simulations and from extrapolation of finite cluster values, respectively. This is in excellent agreement with the often debated (but widely cited) and only available value of 202 K, dating back to measurements by Gray and Ramsay in 1909.

Three-Dimensional Color Code Thresholds via Statistical-Mechanical Mapping.

Three-dimensional (3D) color codes have advantages for fault-tolerant quantum computing, such as protected quantum gates with relatively low overhead and robustness against imperfect measurement of error syndromes. Here we investigate the storage threshold error rates for bit-flip and phase-flip noise in the 3D color code (3DCC) on the body-centered cubic lattice, assuming perfect syndrome measurements. Inparticular, by exploiting a connection between error correction and statistical mechanics, we estimate the threshold for 1D stringlike and 2D sheetlike logical operators to be p_{3DCC}^{(1)}≃1.9% and p_{3DCC}^{(2)}≃27.6%. We obtain these results by using parallel tempering MonteCarlo simulations to study the disorder-temperature phase diagrams of two new 3D statistical-mechanical models: the four- and six-body random coupling Ising models.