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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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At least 199 records · Page 11
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Multiplexed characterization of rationally designed promoter architectures deconstructs combinatorial logic for IPTG-inducible systems

Abstract A crucial step towards engineering biological systems is the ability to precisely tune the genetic response to environmental stimuli. In the case of Escherichia coli inducible promoters, our incomplete understanding of the relationship between sequence composition and gene expression hinders our ability to predictably control transcriptional responses. Here, we profile the expression dynamics of 8269 rationally designed, IPTG-inducible promoters that collectively explore the individual and combinatorial effects of RNA polymerase and LacI repressor binding site strengths. We then fit a statistical mechanics model to measured expression that accurately models gene expression and reveals properties of theoretically optimal inducible promoters. Furthermore, we characterize three alternative promoter architectures and show that repositioning binding sites within promoters influences the types of combinatorial effects observed between promoter elements. In total, this approach enables us to deconstruct relationships between inducible promoter elements and discover practical insights for engineering inducible promoters with desirable characteristics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Sampling lattices in semi-grand canonical ensemble with autoregressive machine learning

Calculating thermodynamic potentials and observables efficiently and accurately is key for the application of statistical mechanics simulations to materials science. However, naive Monte Carlo approaches, on which such calculations are often dependent, struggle to scale to complex materials in many state-of-the-art disciplines such as the design of high entropy alloys or multi-component catalysts. To address this issue, we adapt sampling tools built upon machine learning-based generative modeling to the materials space by transforming them into the semi-grand canonical ensemble. Furthermore, we show that the resulting models are transferable across wide ranges of thermodynamic conditions and can be implemented with any internal energy model U, allowing integration into many existing materials workflows. We demonstrate the applicability of this approach to the simulation of benchmark systems (AgPd, CuAu) that exhibit diverse thermodynamic behavior in their phase diagrams. Finally, we discuss remaining challenges in model development and promising research directions for future improvements.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Mean force kinetic theory applied to self-diffusion in supercritical Lennard-Jones fluids

A new kinetic-theory-based calculation of the self-diffusion coefficient for dense supercritical Lennard-Jones fluids is presented. The mean force kinetic theory, which was recently developed for transport in dense plasmas, is applied for the calculation of diffusion in dense neutral fluids. The calculation only requires the pair distribution function, a quantity that is readily calculable from equilibrium statistical mechanics for many systems, including the Lennard-Jones fluid. The self-diffusion coefficients are compared with calculations from molecular dynamics simulations, and good agreement at high density is demonstrated, even in the vicinity of the solid–fluid coexistence line. A comparison of different kinetic models with molecular dynamics simulations demonstrates that the transport coefficients have important contributions due to particle interaction via a potential of mean force and local correlations, which increase the collision rate. The new calculations compare well to those from free-volume theory and overcome a limitation of this theory that prevents its use in systems that interact via long range monotonic potentials. It is expected that this approach will also apply to other systems, including neutral-plasma and neutral-electrolyte mixtures.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

Renormalized site density functional theory for models of ion hydration

Development of accurate statistical mechanics models of molecular liquid systems is a problem of great practical and fundamental importance. Site-density functional theory (SDFT) is one of the promising directions in this area, but its success hinges upon the ability to efficiently reconcile co-existence of two distinct intra- and inter-molecular interaction regimes in a molecular liquid. Renormalized formulation of site-density functional theory (RSDFT), that we have recently developed, resolves this problem by introducing an additional potential field variable that decouples two interaction scales and maps the molecular liquid problem onto the effective simple liquid mixture. This work provides a critical assessment of RSDFT for the hydrated ion system - a problem, which historically has always been one of the most difficult cases for SDFT applications. Using two-site model of water, we perform a comprehensive analysis of hydrated alkali metal and halogen ions, including both structural and free energy based characteristics. The results indicate that RSDFT provides a significant improvement over conventional 3D-RISM implementations, and may prove useful in coarse grained simulations based on two-site solvent models.

Chuev, Gennady N.↗
DOE OSTI2022

Renormalization of excitonic properties by polar phonons

Here we employ quasiparticle path integral molecular dynamics to study how the excitonic properties of model semiconductors are altered by electron–phonon coupling. We describe ways within a path integral representation of the system to evaluate the renormalized mass, binding energy, and radiative recombination rate of excitons in the presence of a fluctuating lattice. To illustrate this approach, we consider Fröhlich-type electron–phonon interactions and employ an imaginary time influence functional to incorporate phonon-induced effects nonperturbatively. The effective mass and binding energies are compared with perturbative and variational approaches, which provide qualitatively consistent trends. We evaluate electron-hole recombination rates as mediated through both trap-assisted and bimolecular processes, developing a consistent statistical mechanical approach valid in the reaction limited regime. These calculations demonstrate how phonons screen electron–hole interactions, generically reducing exciton binding energies and increasing their radiative lifetimes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Dynamic density functional theory of polymers with salt in electric fields

Here we present a dynamic density functional theory for modeling the effects of applied electric fields on the local structure of polymers with added salt (polymer electrolytes). Time-dependent equations for the local electrostatic potential and volume fractions of polymer, cation, and anion of added salt are developed using the principles of linear irreversible thermodynamics. For such a development, a field theoretic description of the free energy of polymer melts doped with salts is used, which captures the effects of local variations in the dielectric function. Connections of the dynamic density functional theory with experiments are established by relating the three phenomenological Onsager’s transport coefficients of the theory to the mutual diffusion of electrolyte, ionic conductivity, and transference number of one of the ions. The theory is connected with a statistical mechanical model developed by Bearman and Kirkwood [J. Chem. Phys. 28, 136 (1958)] after relating the three transport coefficients to friction coefficients. The steady-state limit of the dynamic density functional theory is used to understand the effects of dielectric inhomogeneity on the phase separation in polymer electrolytes. The theory developed here provides not only a way to connect with experiments but also to develop multi-scale models for studying connections between local structure and ion transport in polymer electrolytes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Murray Gell-Mann

Murray Gell-Mann, the preeminent architect of theoretical elementary-particle physics, died on 24 May 2019 in Santa Fe, New Mexico. He received the 1969 Nobel Prize “for his contributions and discoveries concerning the classification of elementary particles and their interactions.” His contributions to physics include many foundational ideas, such as the renormalization group, which is fundamental to quantum field theory and statistical mechanics.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Signatures of a liquid–liquid transition in an ab initio deep neural network model for water

Significance Water is central across much of the physical and biological sciences and exhibits physical properties that are qualitatively distinct from those of most other liquids. Understanding the microscopic basis of water’s peculiar properties remains an active area of research. One intriguing hypothesis is that liquid water can separate into metastable high- and low-density liquid phases at low temperatures and high pressures, and the existence of this liquid–liquid transition could explain many of water’s anomalous properties. We used state-of-the-art approaches in computational quantum chemistry, statistical mechanics, and machine learning and obtained evidence consistent with a liquid–liquid transition, supporting the argument for the existence of this phenomenon in real water.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Berni Julian Alder, theoretical physicist and inventor of molecular dynamics, 1925–2020

Berni Julian Alder, one of the leading figures in the invention of molecular dynamics simulations used for a wide array of problems in physics and chemistry, died on September 7th, 2020. His career, spanning more than 65 years, transformed statistical mechanics, many body physics, the study of chemistry and the microscopic dynamics of fluids, by making atomistic computational simulation (in parallel with traditional theory and experiment) a new pathway to unexpected discoveries. Among his many honors, the CECAM prize, recognizing exceptional contributions to the simulation of the microscopic properties of matter is named for him. He was awarded the National Medal of Science by President Obama in 2008.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Elucidation of the physical factors that control activated transport of penetrants in chemically complex glass-forming liquids

Understanding the activated transport of penetrant or tracer atoms and molecules in condensed phases is a challenging problem in chemistry, materials science, physics, and biophysics. Many angstrom- and nanometer-scale features enter due to the highly variable shape, size, interaction, and conformational flexibility of the penetrant and matrix species, leading to a dramatic diversity of penetrant dynamics. Based on a minimalist model of a spherical penetrant in equilibrated dense matrices of hard spheres, a recent microscopic theory that relates hopping transport to local structure has predicted a novel correlation between penetrant diffusivity and the matrix thermodynamic dimensionless compressibility, S 0 ( T ) (which also quantifies the amplitude of long wavelength density fluctuations), as a consequence of a fundamental statistical mechanical relationship between structure and thermodynamics. Moreover, the penetrant activation barrier is predicted to have a factorized/multiplicative form, scaling as the product of an inverse power law of S 0 ( T ) and a linear/logarithmic function of the penetrant-to-matrix size ratio. This implies an enormous reduction in chemical complexity that is verified based solely on experimental data for diverse classes of chemically complex penetrants dissolved in molecular and polymeric liquids over a wide range of temperatures down to the kinetic glass transition. The predicted corollary that the penetrant diffusion constant decreases exponentially with inverse temperature raised to an exponent determined solely by how S 0 ( T ) decreases with cooling is also verified experimentally. Our findings are relevant to fundamental questions in glassy dynamics, self-averaging of angstrom-scale chemical features, and applications such as membrane separations, barrier coatings, drug delivery, and self-healing.

Science & Technology - Other Topics↗
DOE OSTI2024

Transport coefficient approach for characterizing nonequilibrium dynamics in soft matter

Nonequilibrium states in soft condensed matter require a systematic approach to characterize and model materials, enhancing predictability and applications. Among the tools, X-ray photon correlation spectroscopy (XPCS) provides exceptional temporal and spatial resolution to extract dynamic insight into the properties of the material. However, existing models might overlook intricate details. We introduce an approach for extracting the transport coefficient, denoted as $J(t)$, from the XPCS studies. This coefficient is a fundamental parameter in nonequilibrium statistical mechanics and is crucial for characterizing transport processes within a system. Our method unifies the Green–Kubo formulas associated with various transport coefficients, including gradient flows, particle–particle interactions, friction matrices, and continuous noise. We achieve this by integrating the collective influence of random and systematic forces acting on the particles within the framework of a Markov chain. We initially validated this method using molecular dynamics simulations of a system subjected to changes in temperatures over time. Subsequently, we conducted further verification using experimental systems reported in the literature and known for their complex nonequilibrium characteristics. The results, including the derived $J(t)$ and other relevant physical parameters, align with the previous observations and reveal detailed dynamical information in nonequilibrium states. This approach represents an advancement in XPCS analysis, addressing the growing demand to extract intricate nonequilibrium dynamics. Further, the methods presented are agnostic to the nature of the material system and can be potentially expanded to hard condensed matter systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2020

Machine learning for collective variable discovery and enhanced sampling in biomolecular simulation

Classical molecular dynamics simulates the time evolution of molecular systems through the phase space spanned by the positions and velocities of the constituent atoms. Molecular-level thermodynamic, kinetic, and structural data extracted from the resulting trajectories provide valuable information for the understanding, engineering, and design of biological and molecular materials. The cost of simulating many-body atomic systems makes simulations of large molecules prohibitively expensive, and the high-dimensionality of the resulting trajectories presents a challenge for analysis. Driven by advances in algorithms, hardware, and data availability, there has been a flare of interest in recent years in the applications of machine learning – especially deep learning – to molecular simulation. Furthermore, these techniques have demonstrated great power and flexibility in both extracting mechanistic understanding of the important nonlinear collective variables governing the dynamics of a molecular system, and in furnishing good low-dimensional system representations with which to perform enhanced sampling or develop long-timescale dynamical models. It is the purpose of this article to introduce the key machine learning approaches, describe how they are married with statistical mechanical theory into domain-specific tools, and detail applications of these approaches in understanding and accelerating biomolecular simulation.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2020

Flat-histogram extrapolation as a useful tool in the age of big data

In this work, we review recent work by the authors to revisit the concept of extrapolating thermodynamic properties of classical systems using statistical mechanical principles. Specifically, we discuss how the combination of these principles with biased sampling techniques enables the prediction of free energy landscapes and other detailed information, such as structural properties, of the system in question. Remarkably accurate estimates of physical properties across a broad range of conditions have been achieved using this approach, greatly reducing the number of simulations needed to explore a given system's behaviour. While approximate, these extrapolations significantly amplify the amount of reasonably accurate information that can be extracted from simulations enabling a small set of them to feed data-intensive regression algorithms such as neural networks. Thus, this extrapolation methodology represents a useful tool for performing tasks such as high-throughput screening of physical properties, optimising force field parameters, exploring equilibrium phase behaviour, and enabling theory-guided data science for these systems.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Renormalized site density functional theory

Site density functional theory (SDFT) provides a rigorous framework for statistical mechanics analysis of inhomogeneous molecular liquids. The key defining feature of these systems is the presence of two very distinct interactions scales (intra- and inter-molecular), and as such proper description of both effects is critical to the accuracy of the calculations. Current SDFT applications utilize the same approximation scheme for both interaction motifs, which negatively impacts the results. Dual space methodology, used in this work, alleviates this issue by providing the flexibility of evaluating part of the interactions in traditional field representation. For molecular liquid this translates into retaining density representation for inter-molecular interactions but describing stiff intra-molecular remainder by more appropriate conventional field based methods. This opens the way to decouple analysis of the two interactions scales - the idea which is developed further in this work for the case of homogeneous reference approximation of inter-molecular interactions. We demonstrate that by defining new collective variables, the behavior of the original molecular liquid system at the inter-molecular level can be transformed to resemble that of an effective simple fluid mixture. The latter is linked to intra-molecular scale through renormalized interaction parameters. We illustrate this renormalization procedure for several types of diatomic liquids, showing that this approach cures many of the shortcomings of existing SDFT methods.

Chuev, Gennady N.↗
DOE OSTI2025

A kinetic-based regularization method for data science applications

We propose a physics-based regularization technique for function learning, inspired by statistical mechanics. By drawing an analogy between optimizing the parameters of an interpolator and minimizing the energy of a system, we introduce corrections that impose constraints on the lower-order moments of the data distribution. This minimizes the discrepancy between the discrete and continuum representations of the data, in turn allowing to access more favorable energy landscapes, thus improving the accuracy of the interpolator. Our approach improves performance in both interpolation and regression tasks, even in high-dimensional spaces. Unlike traditional methods, it does not require empirical parameter tuning, making it particularly effective for handling noisy data. We also show that thanks to its local nature, the method offers computational and memory efficiency advantages over Radial Basis Function interpolators, especially for large datasets.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2025

Convex relaxation for Fokker–Planck equation

We propose an approach to directly estimate the moments or marginals for a high-dimensional equilibrium distribution in statistical mechanics by solving the high-dimensional Fokker–Planck equation in terms of low-order cluster moments or marginals. With this approach, we bypass the exponential complexity of estimating the full high-dimensional distribution and directly solve the simplified partial differential equations for low-order moments/marginals. Moreover, the proposed moment/marginal relaxation is fully convex and can be solved via off-the-shelf solvers. We further propose a time-dependent version of the convex programs to study non-equilibrium dynamics. In a specific setting, we show the proposed method can recover a mean-field-type equilibrium density. Numerical results are provided to demonstrate the performance of the proposed algorithm for high-dimensional systems.

Chen, Yian↗
DOE OSTI2025

Exact spectral gaps of random one-dimensional quantum circuits

The spectral gap of local random quantum circuits is a fundamental property that determines how close the moments of the circuit's unitaries match those of a Haar random distribution. When studying spectral gaps, it is common to bound these quantities using tools from statistical mechanics or via quantum information-based inequalities. Here, by focusing on the second moment of one-dimensional unitary circuits where nearest-neighboring gates act on sets of qudits (with open and closed boundary conditions), we show that one can exactly compute the associated spectral gaps. Indeed, having access to their functional form allows us to prove several important results, such as the fact that the spectral gap for closed boundary condition is exactly the square of the gap for open boundaries, as well as improve on previously known bounds for approximate design convergence. Finally, we verify our theoretical results by numerically computing the spectral gap for systems of up to 70 qubits, as well as comparing them to gaps of random orthogonal and symplectic circuits.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2020

Mean-field entanglement transitions in random tree tensor networks

Entanglement phase transitions in quantum chaotic systems subject to projective measurements and in random tensor networks have emerged as a new class of critical points separating phases with different entanglement scaling. We propose a mean-field theory of such transitions by studying the entanglement properties of random tree tensor networks. As a function of bond dimension, we find a phase transition separating area-law from logarithmic scaling of the entanglement entropy. Using a mapping onto a replica statistical mechanics model defined on a Cayley tree and the cavity method, we analyze the scaling properties of such transitions. Our approach provides a tractable, mean-field-like example of an entanglement transition. Furthermore, we verify our predictions numerically by computing directly the entanglement of random tree tensor network states.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗