Publications
Publications by categories in reversed chronological order.
2025
- arXivAdsorbate phase transitions on nanoclusters from nested samplingThanawitch Chatbipho, Ray Yang, Robert B Wexler, and 1 more authorarXiv preprint arXiv:2506.01295, Jun 2025
Nested sampling was employed to investigate adsorption equilibria on the truncated-octahedral Lennard-Jones nanocluster LJ38 while systematically varying adsorbate-surface well depth and Lennard-Jones size parameters. Evaluation of the canonical partition function over a wide temperature range identifies two successive phase transitions: (i) condensation of the gas phase onto the cluster surface at higher temperatures, and (ii) lateral rearrangement of the adsorbed layer at lower temperatures. For identical interactions, the condensate first populates both three- and four-fold hollow sites; when adsorbate-adsorbate interactions are weakened, preference shifts to the four-coordinated (100) sites. Size mismatch governs low-temperature behavior: smaller adsorbates aggregate to increase mutual contacts, whereas larger ones distribute more evenly to maximize coordination with the cluster. These findings highlight key trends in facet competition and lattice mismatch, and showcase nested sampling as an automated, unbiased tool for exploring surface configurational space and guiding investigations of more complex, realistic interfaces.
@article{chatbipho2025adsorbate, title = {Adsorbate phase transitions on nanoclusters from nested sampling}, author = {Chatbipho, Thanawitch and Yang, Ray and Wexler, Robert B and P{\'a}rtay, Livia B}, journal = {arXiv preprint arXiv:2506.01295}, doi = {10.48550/arXiv.2506.01295}, year = {2025}, month = jun }
2024
- PCCPSurface Phase Diagrams from Nested SamplingMingrui Yang, Livia B. Pártay, and Robert B. WexlerPhysical Chemistry Chemical Physics, May 2024
Studies in atomic-scale modeling of surface phase equilibria often focus on temperatures near zero Kelvin due to the challenges in calculating the free energy of surfaces at finite temperatures. The Bayesian-inference-based nested sampling (NS) algorithm allows for modeling phase equilibria at arbitrary temperatures by directly and efficiently calculating the partition function, whose relationship with free energy is well known. This work extends NS to calculate adsorbate phase diagrams, incorporating all relevant configurational contributions to the free energy. We apply NS to the adsorption of Lennard-Jones (LJ) gas particles on low-index and vicinal LJ solid surfaces and construct the canonical partition function from these recorded energies to calculate ensemble averages of thermodynamic properties, such as the constant-volume heat capacity and order parameters that characterize the structure of adsorbate phases. Key results include determining the nature of phase transitions of adsorbed LJ particles on flat and stepped LJ surfaces, which typically feature an enthalpy-driven condensation at higher temperatures and an entropy-driven reordering process at lower temperatures, and the effect of surface geometry on the presence of triple points in the phase diagrams. Overall, we demonstrate the ability and potential of NS for surface modeling.
@article{yangSurfacePhaseDiagrams2024, title = {Surface Phase Diagrams from Nested Sampling}, author = {Yang, Mingrui and P{\'a}rtay, Livia B. and Wexler, Robert B.}, year = {2024}, month = may, journal = {Physical Chemistry Chemical Physics}, volume = {26}, number = {18}, pages = {13862--13874}, publisher = {The Royal Society of Chemistry}, issn = {1463-9084}, doi = {10.1039/D4CP00050A}, urldate = {2024-08-16}, copyright = {All rights reserved}, langid = {english}, }
2022
- PRBStochastic Differential Equation Approach to Understanding the Population Control Bias in Full Configuration Interaction Quantum Monte CarloJoachim Brand, Mingrui Yang, and Elke PahlPhysical Review B, Jun 2022
We investigate a systematic statistical bias found in full configuration quantum Monte Carlo (FCIQMC) that originates from controlling a walker population with a fluctuating shift parameter. This bias can become the dominant error when the sign problem is absent, e.g., in bosonic systems. FCIQMC is a powerful statistical method for obtaining information about the ground state of a sparse and abstract matrix. We show that, when the sign problem is absent, the shift estimator has the nice property of providing an upper bound for the exact ground-state energy and all projected energy estimators, while a variational estimator is still an upper bound to the exact energy with substantially reduced bias. A scalar model of the general FCIQMC population dynamics leads to an exactly solvable Itô stochastic differential equation. It provides further insights into the nature of the bias and gives accurate analytical predictions for delayed cross-covariance and autocovariance functions of the shift energy estimator and the walker number. The model provides a toehold on finding a cure for the population control bias. We provide evidence for nonuniversal power-law scaling of the population control bias with walker number in the Bose-Hubbard model for various estimators of the ground-state energy based on the shift or on projected energies. For the specific case of the noninteracting Bose-Hubbard Hamiltonian we obtain a full analytical prediction for the bias of the shift energy estimator.
@article{brandStochasticDifferentialEquation2022, title = {Stochastic Differential Equation Approach to Understanding the Population Control Bias in Full Configuration Interaction Quantum {{Monte Carlo}}}, author = {Brand, Joachim and Yang, Mingrui and Pahl, Elke}, year = {2022}, month = jun, journal = {Physical Review B}, volume = {105}, number = {23}, pages = {235144}, issn = {2469-9950, 2469-9969}, doi = {10.1103/PhysRevB.105.235144}, urldate = {2023-06-22}, copyright = {All rights reserved}, langid = {english}, }
- Cond. Mat.Polaron-Depleton Transition in the Yrast Excitations of a One-Dimensional Bose Gas with a Mobile ImpurityMingrui Yang, Matija Čufar, Elke Pahl, and 1 more authorCondensed Matter, Mar 2022
We present exact numerical data for the lowest-energy momentum eigenstates (yrast states) of a repulsive spin impurity in a one-dimensional Bose gas using full configuration interaction quantum Monte Carlo (FCIQMC). As a stochastic extension of exact diagonalization, it is well suited for the study of yrast states of a lattice-renormalized model for a quantum gas. Yrast states carry valuable information about the dynamic properties of slow-moving mobile impurities immersed in a many-body system. Based on the energies and the first and second-order correlation functions of yrast states, we identify different dynamical regimes and the transitions between them: The polaron regime, where the impurity’s motion is affected by the Bose gas through a renormalized effective mass; a regime of a gray soliton that is weakly correlated with a stationary impurity, and the depleton regime, where the impurity occupies a dark or gray soliton. Extracting the depleton effective mass reveals a super heavy regime where the magnitude of the (negative) depleton mass exceeds the mass of the finite Bose gas.
@article{yangPolaronDepletonTransitionYrast2022, title = {Polaron-{{Depleton Transition}} in the {{Yrast Excitations}} of a {{One-Dimensional Bose Gas}} with a {{Mobile Impurity}}}, author = {Yang, Mingrui and {\v C}ufar, Matija and Pahl, Elke and Brand, Joachim}, year = {2022}, month = mar, journal = {Condensed Matter}, volume = {7}, number = {1}, pages = {15}, publisher = {Multidisciplinary Digital Publishing Institute}, issn = {2410-3896}, doi = {10.3390/condmat7010015}, urldate = {2022-06-21}, copyright = {http://creativecommons.org/licenses/by/3.0/}, langid = {english}, keywords = {,dimensional Bose gas,impurity,one,one-dimensional bose gas,one-dimensional Bose gas,quantum monte carlo,quantum Monte Carlo,yrast states}, }
2021
- PCCPA Theoretical Investigation of 38-Atom CuPd Clusters: The Effect of Potential Parameterisation on Structure and SegregationCaitlin A. Casey-Stevens, Mingrui Yang, Geoffrey R. Weal, and 3 more authorsPhysical Chemistry Chemical Physics, Mar 2021
Understanding the structure of bimetallic clusters is increasingly important due to their emerging practical applications. Herein we investigate the structure of 38-atom CuPd clusters using a genetic algorithm with cluster energies described by the semi-empirical Gupta potential. Selected clusters are then refined with density functional theory. Three different parameterisations of the Gupta potential are used and their performance assessed to understand what features of bulk and surfaces are necessary to capture for accurate description of small clusters. Three general regions of motif stability exist; for the Pd majority clusters (Pd38 to Cu4Pd34) the truncated octahedron is most stable, while for clusters of intermediate compositions (Cu5Pd33 to Cu25Pd13) a “pancake” icosahedron is most stable, and for the Cu majority clusters (Cu26Pd12 to Cu38) again the truncated octahedron is most stable. CuPd clusters tend to segregate to a Cu-core, Pd-shell structure if possible, and at higher Cu compositions, the Pd segregates to the faces of the cluster. Using multiple parameterisations of the Gupta potential ensures the full variety of possible structures is found, and improves the search for the most stable CuPd clusters.
@article{a.casey-stevensTheoreticalInvestigation38atom2021, title = {A Theoretical Investigation of 38-Atom {{CuPd}} Clusters: The Effect of Potential Parameterisation on Structure and Segregation}, shorttitle = {A Theoretical Investigation of 38-Atom {{CuPd}} Clusters}, author = {{A.~Casey-Stevens}, Caitlin and Yang, Mingrui and R.~Weal, Geoffrey and M.~McIntyre, Samantha and K.~Nally, Brianna and L.~Garden, Anna}, year = {2021}, journal = {Physical Chemistry Chemical Physics}, volume = {23}, number = {30}, pages = {15950--15964}, publisher = {Royal Society of Chemistry}, doi = {10.1039/D1CP00810B}, urldate = {2024-08-16}, copyright = {All rights reserved}, langid = {english}, }
2020
- JCPImproved Walker Population Control for Full Configuration Interaction Quantum Monte CarloMingrui Yang, Elke Pahl, and Joachim BrandThe Journal of Chemical Physics, Nov 2020
Full configuration interaction quantum Monte Carlo (FCIQMC) is a stochastic approach for finding the ground state of a quantum manybody Hamiltonian. It is based on the dynamical evolution of a walker population in Hilbert space, which samples the ground state configuration vector over many iterations. Here, we present a modification of the original protocol for walker population control of Booth et al. [J. Chem. Phys. 131, 054106 (2009)] in order to achieve equilibration at a pre-defined average walker number and to avoid walker number overshoots. The dynamics of the walker population is described by a noisy damped harmonic oscillator and controlled by two parameters responsible for damping and forcing, respectively, for which reasonable values are suggested. We further introduce a population growth witness that can be used to detect annihilation plateaus related to overcoming the FCIQMC sign problem. Features of the new population control procedure such as precise walker number control and fast equilibration are demonstrated. The standard error of the shift estimator for the ground state energy as well as the population control bias is found to be unaffected by the population control procedure or its parameters. The improved control of the walker number, and thereby memory consumption, is a desirable feature required for automating FCIQMC calculations and requires minimal modifications to the existing code.
@article{yangImprovedWalkerPopulation2020, title = {Improved Walker Population Control for Full Configuration Interaction Quantum {{Monte Carlo}}}, author = {Yang, Mingrui and Pahl, Elke and Brand, Joachim}, year = {2020}, month = nov, journal = {The Journal of Chemical Physics}, volume = {153}, number = {17}, pages = {174103}, issn = {0021-9606, 1089-7690}, doi = {10.1063/5.0023088}, urldate = {2023-06-22}, copyright = {All rights reserved}, langid = {english}, keywords = {,FCIQMC,Quantum Gases}, }
2019
- Chem. Asian J.Predictable Electronic Tuning By Choice of Azine Substituent in Five Iron(II) Triazoles: Redox Properties and DFT CalculationsSantiago Rodríguez-Jiménez, Luca Bondì, Mingrui Yang, and 2 more authorsChemistry – An Asian Journal, Nov 2019
Five new mononuclear iron(II) tris-ligand complexes, and four solvatomorphs, have been made from the azine-substituted 1,2,4-triazole ligands (Lazine): [FeII(Lpyridazine)3](BF4)2 (1), [FeII(Lpyrazine)3](BF4)2 (2), [FeII(Lpyridine)3](BF4)2 (3), [FeII(L2pyrimidine)3](BF4)2 (4), and [FeII(L4pyrimidine)3](BF4)2 (5). Single-crystal XRD and solid-state magnetometry reveal that all of them are low-spin (LS) iron(II), except for solvatomorph 5⋅4 H2O. Evans method NMR studies in CD2Cl2, (CD3)2CO and CD3CN show that all are LS in these solvents, except 5 in CD2Cl2 (consistent with L4pyrimidine imposing the weakest field). Cyclic voltammetry in CH3CN vs. Ag/0.01 m AgNO3 reveals an, at best quasi-reversible, FeIII/II redox process, with Epa increasing from 0.69 to 0.99 V as the azine changes: pyridine< pyridazine<2-pyrimidine<4-pyrimidine< pyrazine. The observed Epa values correlate linearly with the DFT calculated HOMO energies for the LS complexes.
@article{rodriguez-jimenezPredictableElectronicTuning2019, title = {Predictable {{Electronic Tuning By Choice}} of {{Azine Substituent}} in {{Five Iron}}({{II}}) {{Triazoles}}: {{Redox Properties}} and {{DFT Calculations}}}, shorttitle = {Predictable {{Electronic Tuning By Choice}} of {{Azine Substituent}} in {{Five Iron}}({{II}}) {{Triazoles}}}, author = {{Rodr{\'i}guez-Jim{\'e}nez}, Santiago and Bond{\`i}, Luca and Yang, Mingrui and Garden, Anna L. and Brooker, Sally}, year = {2019}, journal = {Chemistry -- An Asian Journal}, volume = {14}, number = {8}, pages = {1158--1166}, issn = {1861-471X}, doi = {10.1002/asia.201801537}, urldate = {2024-08-16}, copyright = {{\copyright} 2019 Wiley-VCH Verlag GmbH \& Co. KGaA, Weinheim}, langid = {english}, keywords = {azine,density functional calculations,Evans method,iron,redox chemistry,triazoles}, }
2017
- JACSA Simple Method of Predicting Spin State in SolutionSantiago Rodríguez-Jiménez, Mingrui Yang, Ian Stewart, and 2 more authorsJournal of the American Chemical Society, Dec 2017
A simple method, using density functional theory (DFT), of predicting spin-state in advance of synthesis is reported. Specifically, an excellent correlation is observed between the switching temperatures (T1/2) in CDCl3 solution of five spin-crossover (SCO)-active [FeII(Lazine)2(NCBH3)2] complexes and the DFT-calculated (and observed) 15N NMR chemical shift (δNA) of the five different azine-substituted 1,2,4-triazole ligands employed, Lazine = 4-(4-methylphenyl)-3-phenyl-5-(azine)-1,2,4-triazole, where azine = pyridine, pyridazine, 4-pyrimidine, pyrazine, and 2-pyrimidine. To test the generality of this finding, DFT was also employed to readily predict the δNA values for a family of 16 literature ligands, known as bppX,Y [X,Y-substituted 2,6-(pyrazol-1-yl)pyridines], which have produced 16 SCO-active [FeII(bppX,Y)2](Z)2 complexes (Z = BF4 or in one case PF6) in (CD3)2CO solution: again an excellent correlation was found between the computed δNA and the observed T1/2. These correlations represent a key advance in the field, as they allow a simple DFT calculation on a modified ligand to be used to reliably predict, before synthesis of the ligand or complex, the T1/2 that would result from that modification. Achieving such easily predictable tuning of T1/2, and hence of spin-state, is a significant step forward in the field of SCO and also has big implications in many other fields in which spin-state is key, including catalysis, metallo-enzyme modeling studies, and host-guest chemistry.
@article{Rodriguez-Jimenez2017, title = {A {{Simple Method}} of {{Predicting Spin State}} in {{Solution}}}, author = {{Rodr{\'i}guez-Jim{\'e}nez}, Santiago and Yang, Mingrui and Stewart, Ian and Garden, Anna L. and Brooker, Sally}, year = {2017}, month = dec, journal = {Journal of the American Chemical Society}, volume = {139}, number = {50}, pages = {18392--18396}, publisher = {American Chemical Society}, issn = {15205126}, doi = {10.1021/jacs.7b11069}, urldate = {2020-11-11}, copyright = {All rights reserved}, pmid = {29156884}, }