Statistical mechanics of a collisionless self- gravitating system.
Computer experiments with one dimensional model, determining self gravitating system approach to Lynden-Bell distribution
Campbell, J. W.↗
SEARCH · Engineering Papers
Results for “computational statistical mechanics”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Development of a Computational Chemical Vapor Deposition Model: Applications to Indium Nitride and Dicyanovinylaniline
A computational chemical vapor deposition (CVD) model is presented, that couples chemical reaction mechanisms with fluid dynamic simulations for vapor deposition experiments. The chemical properties of the systems under investigation are evaluated using quantum, molecular and statistical mechanics models. The fluid dynamic computations are performed using the CFD-ACE program, which can simulate multispecies transport, heat and mass transfer, gas phase chemistry, chemistry of adsorbed species, pulsed reactant flow and variable gravity conditions. Two experimental setups are being studied, in order to fabricate films of: (a) indium nitride (InN) from the gas or surface phase reaction of trimethylindium and ammonia; and (b) 4-(1,1)dicyanovinyl-dimethylaminoaniline (DCVA) by vapor deposition. Modeling of these setups requires knowledge of three groups of properties: thermodynamic properties (heat capacity), transport properties (diffusion, viscosity, and thermal conductivity), and kinetic properties (rate constants for all possible elementary chemical reactions). These properties are evaluated using computational methods whenever experimental data is not available for the species or for the elementary reactions. The chemical vapor deposition model is applied to InN and DCVA. Several possible InN mechanisms are proposed and analyzed. The CVD model simulations of InN show that the deposition rate of InN is more efficient when pulsing chemistry is used under conditions of high pressure and microgravity. An analysis of the chemical properties of DCVA show that DCVA dimers may form under certain conditions of physical vapor transport. CVD simulations of the DCVA system suggest that deposition of the DCVA dimer may play a small role in the film and crystal growth processes.
Cardelino, Carlos↗
Multiscale Modeling Meets Machine Learning: What Can We Learn?
Machine learning is increasingly recognized as a promising technology in the biological, biomedical, and behavioral sciences. There can be no argument that this technique is incredibly successful in image recognition with immediate applications in diagnostics including electrophysiology, radiology, or pathology, where we have access to massive amounts of annotated data. However, machine learning often performs poorly in prognosis, especially when dealing with sparse data. This is a field where classical physics-based simulation seems to remain irreplaceable. In this review, we identify areas in the biomedical sciences where machine learning and multiscale modeling can mutually benefit from one another: Machine learning can integrate physics-based knowledge in the form of governing equations, boundary conditions, or constraints to manage ill-posted problems and robustly handle sparse and noisy data; multiscale modeling can integrate machine learn- ing to create surrogate models, identify system dynamics and parameters, analyze sensitivities, and quantify uncertainty to bridge the scales and understand the emergence of function. With a view towards applications in the life sciences, we discuss the state of the art of combining machine learning and multiscale modeling, identify applications and opportunities, raise open questions, and address potential challenges and limitations. We anticipate that it will stimulate discussion within the community of computational mechanics and reach out to other disciplines including mathematics, statistics, computer science, artificial intelligence, biomedicine, systems biology, and precision medicine to join forces towards creating robust and efficient models for biological systems.
machine learning, multiscale modeling, physics-bas↗
Radial distribution functions for the gaussian model.
Comparison of monte carlo, percus-yevick integral equations and convolution-hypernetted-chain methods for computing radial distribution functions of gaussian model
RADIAL DISTRIBUTION↗
Modern chemical graph theory
Abstract Graph theory has a long history in chemistry. Yet as the breadth and variety of chemical data is rapidly changing, so too do graph encoding methods and analyses that yield qualitative and quantitative insights. Using illustrative cases within a basic mathematical framework, we showcase modern chemical graph theory's utility in Chemists' analysis and model development toolkit. The encoding of both experimental and simulation data is discussed at various levels of granularity of information. This is followed by a discussion of the two major classes of graph theoretical analyses: identifying connectivity patterns and partitioning methods. Measures, metrics, descriptors, and topological indices are then introduced with an emphasis upon enhancing interpretability and incorporation into physical models. Challenging data cases are described that include strategies for studying time dependence. Throughout, we incorporate recent advancements in computer science and applied mathematics that are propelling chemical graph theory into new domains of chemical study. This article is categorized under: Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods Structure and Mechanism > Computational Materials Science Structure and Mechanism > Molecular Structures
Leite, Leonardo S. G.↗
Mana and thermalization: Probing the feasibility of near-Clifford Hamiltonian simulation
Quantum hydrodynamics is the emergent classical dynamics governing transport of conserved quantities in generic strongly interacting quantum systems. Here, recent matrix product operator methods [1,2] have made simulations of quantum hydrodynamics in 1+1D tractable, but they do not naturally generalize to 2+1D or higher, and they offer limited guidance as to the difficulty of simulations on quantum computers. Near-Clifford simulation algorithms are not limited to one dimension, and future error-corrected quantum computers will likely be bottlenecked by non-Clifford operations. We therefore investigate the non-Clifford resource requirements for simulation of quantum hydrodynamics using mana, a resource theory of non-Clifford operations. For infinite-temperature starting states, we find that the mana of subsystems quickly approaches zero, while for starting states with energy above some threshold the mana approaches a nonzero value. Surprisingly, in each case the finite-time mana is governed by the subsystem entropy, not the thermal state mana; we argue that this is because mana is a sensitive diagnostic of finite-time deviations from canonical typicality.
1-dimensional spin chains↗
CASM — A software package for first-principles based study of multicomponent crystalline solids
CASM is a software package that enables first-principles based studies of crystalline materials. It has been designed to treat coupled chemical, mechanical, vibrational, and magnetic degrees of freedom to determine ground state and finite temperature properties of crystals. The symmetry of the underlying parent crystal structure is used to enumerate perturbations of the parent crystal structure and generate derivative structures which can be input to first-principles calculations in order to explore the ground state energy landscape. CASM algorithmically constructs cluster expansions that fully couple discrete and continuous degrees of freedom, and generates highly efficient code to evaluate the cluster expansion basis functions. Widely used machine learning methods are integrated for fitting expansion coefficients to first-principle calculations. The fully parameterized cluster expansions can be combined with (kinetic) Monte Carlo methods to calculate finite temperature thermodynamic and kinetic properties. CASM Alloy Manager identifies distinct parent crystal structures in an alloy system, creating individual projects for each, and integrating the results. The integrated infrastructure facilitates the linkage between first-principles statistical mechanics predictions with higher length scale computational methods, such as phase field simulations. In conclusion, CASM projects are designed to be easy to share in repositories, to re-use, and to extend to include additional chemical species or types of degrees of freedom.
36 MATERIALS SCIENCE↗
Activated relaxation in supercooled monodisperse atomic and polymeric WCA fluids: Simulation and ECNLE theory
Here, we combine simulation and Elastically Collective Nonlinear Langevin Equation (ECNLE) theory to study the activated relaxation in monodisperse atomic and polymeric Weeks–Chandler–Andersen (WCA) liquids over a wide range of temperatures and densities in the supercooled regime under isochoric conditions. By employing novel crystal-avoiding simulations, metastable equilibrium dynamics is probed in the absence of complications associated with size polydispersity. Based on a highly accurate structural input from integral equation theory, ECNLE theory is found to describe well the simulated density and temperature dependences of the alpha relaxation time of atomic fluids using a single system-specific parameter, a c , that reflects the nonuniversal relative importance of local cage and collective elastic barriers. For polymer fluids, the explicit dynamical effect of local chain connectivity is modeled at the fundamental dynamic free energy trajectory level based on a different parameter, N c , that quantifies the degree of intramolecular correlation of bonded segment activated barrier hopping. For the flexible chain model studied, a physically intuitive value of N c ≈ 2 results in good agreement between simulation and theory. A direct comparison between atomic and polymeric systems reveals that chain connectivity can speed up activated segmental relaxation due to weakening of equilibrium packing correlations but can slow down relaxation due to local bonding constraints. The empirical thermodynamic scaling idea for the alpha time is found to work well at high densities or temperatures but fails when both density and temperature are low. The rich and subtle behaviors revealed from simulation for atomic and polymeric WCA fluids are all well captured by ECNLE theory.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
First-Principles Statistical Mechanics Study of Magnetic Fluctuations and Order–Disorder in the Spinel LiNi 0.5 Mn 1.5 O 4 Cathode
While significant magnetic interactions exist in lithium transition metal oxides, commonly used as Li-ion cathodes, the interplay between magnetic couplings, disorder, and redox processes remains poorly understood. In this work, we focus on the high-voltage spinel LiNi 0.5 Mn 1.5 O 4 (LNMO) cathode as a model system on which to apply a computational framework that uses first principles-based statistical mechanics methods to predict the finite temperature magnetic properties of materials and provide insights into the complex interplay between magnetic and chemical degrees of freedom. Density functional theory calculations on multiple distinct Ni–Mn orderings within the LNMO system, including the ordered ground-state structure (space group P4332), reveal a preference for a ferrimagnetic arrangement of the Ni and Mn sublattices due to strong antiferromagnetic superexchange interactions between neighboring Mn 4+ and Ni 2+ ions and ferromagnetic Mn–Mn and Ni–Ni couplings, as revealed by magnetic cluster expansions. These results are consistent with qualitative predictions using the Goodenough-Kanamori-Anderson rules. Simulations of the finite temperature magnetic properties of LNMO are conducted using Metropolis Monte Carlo. We find that a “semiclassical” Monte Carlo sampling method based on the Heisenberg Hamiltonian accurately predicts experimental magnetic transition temperatures observed in magnetometry measurements. This study highlights the importance of a robust computational toolkit that accurately captures the complex chemomagnetic interactions and predicts finite temperature magnetic behavior to help analyze experimental magnetic and magnetic resonance spectroscopy data acquired ex situ and operando.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Resolving local ordering and structure in Mn x Ge 1- x Te alloys through thermodynamic ensembles of pair distribution functions
Characterizing local bonding environments in complex materials is essential for understanding and optimizing their properties. Equally as important is the ability to predict local motifs as a function of synthesis conditions, enhancing chemists’ ability to design properties into materials. In this study, we present an approach to leverage statistical mechanics to generate temperature- and energy-informed ensemble averaged pair distribution functions (PDFs). This method, which we have named Thermodynamic Ensemble Averages of PDFs for Ordering and Transformations (TEAPOT), utilizes density functional theory (DFT) to relax supercells while incorporating energetic penalties for local order, enabling accurate and computationally efficient analysis of local structure. We apply this method to the neutron PDF measurements of the pseudobinary MnTe–GeTe (MGT) alloy, demonstrating its capability to resolve complex local distortions and chemical ordering. Our results reveal detailed insights into phase transformations and local distortions driven by Mn substitution. For compositions that globally present as rock salt, our analysis reveals that Ge coordination geometry is heavily impacted by synthesis temperature. We propose that high temperature synthesis conditions promote a lowered Ge polyhedra distortion, promoting high charge carrier mobility due to the alignment of local and global structure. Incorporating statistical mechanics and computation into experimental analysis thus guides synthesis of tailored local structure.
36 MATERIALS SCIENCE↗
Monitored Fluctuating Hydrodynamics
We introduce a hydrodynamic framework for describing monitored classical stochastic processes. We study the conditional ensembles for these monitored processes—i.e., we compute spacetime correlation functions conditioned on a fixed, typical measurement record. In the presence of global symmetries we show that these conditional ensembles can undergo measurement-induced “sharpening” phase transitions as a function of the monitoring rate; moreover, even weak monitoring can give rise to novel critical phases, derived entirely from a classical perspective. We give a simple hydrodynamic derivation of the known “charge-fuzzy phase” for weakly monitored diffusive many-body quantum systems. We show that although the unmonitored symmetric and asymmetric exclusion processes are in different universality classes of transport, the fluctuations in their conditional ensembles flow to the same fixed point with emergent relativistic invariance under monitoring. On the other hand, weakly monitored systems with non-Abelian symmetries enter a novel strongly coupled fixed point with nontrivial dynamical exponent, which we characterize. Our formalism naturally accounts for monitoring general observables, such as currents or density gradients, and allows for a direct calculation of information-theoretic diagnostics of sharpening transitions, including the Shannon entropy of the measurement record.
classical statistical mechanics↗
Entanglement features of random neural network quantum states
Restricted Boltzmann machines (RBMs) are a class of neural networks that have been successfully employed as a variational ansatz for quantum many-body wave functions. Here, we develop an analytic method to study quantum many-body spin states encoded by random RBMs with independent and identically distributed complex Gaussian weights. By mapping the computation of ensemble-averaged quantities to statistical mechanics models, we are able to investigate the parameter space of the RBM ensemble in the thermodynamic limit. We discover qualitatively distinct wave functions by varying RBM parameters, which correspond to distinct phases in the equivalent statistical mechanics model. Notably, there is a regime in which the typical RBM states have near-maximal entanglement entropy in the thermodynamic limit, similar to that of Haar-random states. However, these states generically exhibit nonergodic behavior in the Ising basis, and do not form quantum state designs, making them distinguishable from Haar-random states.
36 MATERIALS SCIENCE↗
Non-Equilibrium Properties from Equilibrium Free Energy Calculations
Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.
Pohorille, Andrew↗
Asymmetric temperature equilibration with heat flow from cold to hot in a quantum thermodynamic system
A model computational quantum thermodynamic network is constructed with two variable temperature baths coupled by a linker system, with an asymmetry in the coupling of the linker to the two baths. It is found in computational simulations that the baths come to “thermal equilibrium” at different bath energies and temperatures. In a sense, heat is observed to flow from cold to hot. Additionally, a description is given in which a recently defined quantum entropy S univ Q for a pure state “universe” continues to increase after passing through the classical equilibrium point of equal temperatures, reaching a maximum at the asymmetric equilibrium. Thus, a second law account Δ S univ Q ≥ 0 holds for the asymmetric quantum process. In contrast, a von Neumann entropy description fails to uphold the entropy law, with a maximum near when the two temperatures are equal, then a decrease Δ S v N < 0 on the way to the asymmetric equilibrium.
71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
Zentropy Theory for Transformative Functionalities of Magnetic and Superconducting Materials
The proposed research developed the zentropy theory through applications to complex magnetic materials and superconductors under the hypothesis that the emergent properties of complex magnetic materials and superconductors can be predicted by statistical mechanics of ergodic microstates with their partition functions computed from DFT-predicted free energies. The key objective is to develop approaches to systematically determine the types and number of microstates and the supercell size in DFT-based calculations through convergency of macroscopic functionalities, with the incorporation of our mixed-space approach accounting for the interactions between periodic supercells. In addition to use scientific intuitions to guide the design of important microstates, the key innovation of the proposed research is to integrate the domain knowledge and the material-property-descriptor database (MPDD) with 4 million microstates, which is supported by our deep neural network machine learning models (SIPFENN: structure-informed prediction of formation energy using neural networks) and integrated with our high throughput DFT Tool Kit (DFTTK). For complex magnetic materials, one of the objectives is to develop approaches to calculate short-range ordering from the statistical distribution of each microstate. For superconductors, the divergency of quasiparticle effective mass at a quantum critical point will be investigated, and the superconducting and non-superconducting microstates will be delineated through analysis of electronic band structure, density of states, charge density, and Fermi surface.
36 MATERIALS SCIENCE↗
Scalable molecular dynamics on CPU and GPU architectures with NAMD
NAMD is a molecular dynamics program designed for high-performance simulations of very large biological objects on CPU- and GPU-based architectures. NAMD offers scalable performance on petascale parallel supercomputers consisting of hundreds of thousands of cores, as well as on inexpensive commodity clusters commonly found in academic environments. It is written in C++ and leans on Charm++ parallel objects for optimal performance on low-latency architectures. NAMD is a versatile, multipurpose code that gathers state-of-the-art algorithms to carry out simulations in apt thermodynamic ensembles, using the widely popular CHARMM, AMBER, OPLS, and GROMOS biomolecular force fields. Here, we review the main features of NAMD that allow both equilibrium and enhanced-sampling molecular dynamics simulations with numerical efficiency. We describe the underlying concepts utilized by NAMD and their implementation, most notably for handling long-range electrostatics; controlling the temperature, pressure, and pH; applying external potentials on tailored grids; leveraging massively parallel resources in multiple-copy simulations; and hybrid quantum-mechanical/molecular-mechanical descriptions. We detail the variety of options offered by NAMD for enhanced-sampling simulations aimed at determining free-energy differences of either alchemical or geometrical transformations and outline their applicability to specific problems. Last, we discuss the roadmap for the development of NAMD and our current efforts toward achieving optimal performance on GPU-based architectures, for pushing back the limitations that have prevented biologically realistic billion-atom objects to be fruitfully simulated, and for making large-scale simulations less expensive and easier to set up, run, and analyze. NAMD is distributed free of charge with its source code at www.ks.uiuc.edu.
high-performance computing↗
Data-driven learning of Mori–Zwanzig operators for isotropic turbulence
Developing reduced-order models for turbulent flows, which contain dynamics over a wide range of scales, is an extremely challenging problem. In statistical mechanics, the Mori–Zwanzig (MZ) formalism provides a mathematically exact procedure for constructing reduced-order representations of high-dimensional dynamical systems, where the effects due to the unresolved dynamics are captured in the memory kernel and orthogonal dynamics. Turbulence models based on MZ formalism have been scarce due to the limited knowledge of the MZ operators, which originates from the difficulty in deriving MZ kernels for complex nonlinear dynamical systems. In this work, we apply a recently developed data-driven learning algorithm, which is based on Koopman's description of dynamical systems and Mori's linear projection operator, on a set of fully resolved isotropic turbulence datasets to extract the Mori–Zwanzig operators. With data augmentation using known turbulence symmetries, the extracted Markov term, memory kernel, and orthogonal dynamics are statistically converged and the generalized fluctuation–dissipation relation can be verified. The properties of the memory kernel and orthogonal dynamics, and their dependence on the choices of observables are investigated to address the modeling assumptions that are commonly used in MZ-based models. A series of numerical experiments are then constructed using the extracted kernels to evaluate the memory effects on prediction. The results show that the prediction errors are strongly affected by the choice of observables and can be further reduced by including the past history of the observables in the memory kernel.
97 MATHEMATICS AND COMPUTING↗
Measurement-induced criticality in random quantum circuits
We investigate the critical behavior of the entanglement transition induced by projective measurements in (Haar) random unitary quantum circuits. Using a replica approach, we map the calculation of the entanglement entropies in such circuits onto a two-dimensional statistical-mechanics model. In this language, the area- to volume-law entanglement transition can be interpreted as an ordering transition in the statistical-mechanics model. We derive the general scaling properties of the entanglement entropies and mutual information near the transition using conformal invariance. We analyze in detail the limit of infinite on-site Hilbert space dimension in which the statistical-mechanics model maps onto percolation. In particular, we compute the exact value of the universal coefficient of the logarithm of subsystem size in the n th Rényi entropies for n ≥ 1 in this limit using relatively recent results for the conformal field theory describing the critical theory of two-dimensional (2D) percolation, and we discuss how to access the generic transition at finite on-site Hilbert space dimension from this limit, which is in a universality class different from 2D percolation. Here, we also comment on the relation to the entanglement transition in random tensor networks, studied previously in Vasseur et al. [Phys. Rev. B 100, 134203 (2019)].
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗