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Thermodynamics-inspired explanations of artificial intelligence

Nature Communications 2024年第1期15卷 7859页

作者： Mehdi, Shams Tiwary, Pratyush Biophysics Program and Institute for Physical Science and Technology University of Maryland College Park 20742 United States Department of Chemistry and Biochemistry and Institute for Physical Science and Technology University of Maryland College Park 20742 United States University of Maryland Institute for Health Computing Bethesda 20852 MD United States

In recent years, predictive machine learning models have gained prominence across various scientific domains. However, their black-box nature necessitates establishing trust in them before accepting their predictions as accurate. One promising strategy involves employing explanation techniques that elucidate the rationale behind a model’s predictions in a way that humans can understand. However, assessing the degree of human interpretability of these explanations is a nontrivial challenge. In this work, we introduce interpretation entropy as a universal solution for evaluating the human interpretability of any linear model. Using this concept and drawing inspiration from classical thermodynamics, we present Thermodynamics-inspired Explainable Representations of AI and other black-box Paradigms, a method for generating optimally human-interpretable explanations in a model-agnostic manner. We demonstrate the wide-ranging applicability of this method by explaining predictions from various black-box model architectures across diverse domains, including molecular simulations, text, and image classification. © The Author(s) 2024.

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Fused-ring induced end-on orientation in conjugated molecular dyads toward efficient single-component organic solar cells

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Aggregate 2023年第2期4卷 291-299页

作者： Dongdong Xia Shengxi Zhou Wen Liang Tan Safakath Karuthedath Chengyi Xiao Chaowei Zhao Frédéric Laquai Christopher R.McNeill Weiwei Li Institute of Applied Chemistry Jiangxi Academy of SciencesNanchangChina Beijing Advanced Innovation Center for Soft Matter Science and Engineering&State Key Laboratory of Organic-Inorganic Composites Beijing University of Chemical TechnologyBeijingChina Department of Materials Science and Engineering Monash UniversityClaytonAustralia KAUST Solar Center(KSC) Physical Sciences and Engineering Division(PSE)Material Science and Engineering Program(MSE)King Abdullah University of Science and Technology(KAUST)ThuwalSaudi Arabia

The molecular orientations of conjugated materials on the substrate mainly include edge-on,face-on,and ***-on and face-on orientations have been widely observed,while end-on orientation has been rarely *** in organic solar cells(OSCs)charge transport is along the vertical direction,end-on orientation with conjugated backbones perpendicular to the substrate is recognized as the ideal microstructure for *** this work,we for the first time obtained the preferential end-on orientation in a conjugated molecular dyad that contains a conjugated backbone as donor and perylene bisimide side units as *** was realized by introducing a fused-ring structure to replace linear terthiophenes with conjugated backbones,yielding F-MDPBI and L-MDPBI ***,a shifting trend of the molecular orientation from dominating edge-on in L-MDPBI to preferential end-on in F-MDPBI was *** a consequence,vertical charge carrier mobilities in F-MDPBI are one order of magnitude higher than those with preferential edge-on orientation,so single-component OSCs based on this molecular dyad as a single photoactive layer provided a power conversion efficiency of 4.89% compared to 1.70% based on L-MDPBI with preferential edge-on orientation.

关键词： conjugated molecular dyads crystallinity edge-on end-on single-component organic solar cells

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Phase separation and domain crystallinity control enable open-air-printable highly efficient and sustainable organic photovoltaics

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InfoMat 2024年第3期6卷 131-143页

作者： Jie Lv Xiaokang Sun Hua Tang Fei Wang Guangye Zhang Liangxiang Zhu Jiaming Huang Qianguang Yang Shirong Lu Gang Li Frédéric Laquai Hanlin Hu Hoffmann Institute of Advanced Materials Shenzhen Polytechnic UniversityShenzhenthe People's Republic of China Shenzhen Institutes of Advanced Technology Chinese Academy of SciencesShenzhenthe People's Republic of China School of Materials Science and Engineering Xiangtan UniversityXiangtanthe People's Republic of China KAUST Solar Center Physical Sciences and Engineering Division(PSE)Materials Science and Engineering Program(MSE)King Abdullah University of Science and Technology(KAUST)ThuwalKingdom of Saudi Arabia College of New Materials and New Energies Shenzhen Technology UniversityShenzhenthe People's Republic of China Department of Electronic and Information Engineering The Hong Kong Polytechnic UniversityHong Kong SARthe People's Republic of China Department of Material Science and Technology Taizhou UniversityTaizhouthe People's Republic of China

Organic solar cells(OSCs)have emerged as a promising solution for sustainable energy production,offering advantages such as a low carbon footprint,short energy payback period,and compatibility with ***,the use of hazardous solvents continues to dominate the best-performing OSCs,mainly because of the challenges of controlling phase separation and domain crystallinity in *** this study,we combined the solvent vapor treatment of CS2 and thermal annealing to precisely control the phase separation and domain crystallinity in PM6:M-Cl and PM6:O-Cl systems processed with the eco-solvent *** method resulted in a maximum power conversion efficiency(PCE)of 18.4%,which is among the highest values reported for sustainable binary ***,the fabrication techniques were transferred from spin coating in a nitrogen environment to blade printing in ambient air,retaining a PCE of 16.0%,showing its potential for high-throughput and scalable *** addition,a comparative analysis of OSCs processed with hazardous and green solvents was conducted to reveal the differences in phase *** work not only underscores the significance of sustainability in OSCs but also lays the groundwork for unlocking the full potential of open-air-printable sustainable OSCs for commercialization.

关键词： open-air printable organic solar cells sustainability

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Inferring phase transitions and critical exponents from limited observations with Thermodynamic Maps

arXiv

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arXiv 2023年

作者： Herron, Lukas Mondal, Kinjal Schneekloth, John S. Tiwary, Pratyush Biophysics Program Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Chemical Biology Laboratory National Cancer Institute FrederickMD21702 United States Department of Chemistry and Biochemistry Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States

Phase transitions are ubiquitous across life, yet hard to quantify and describe accurately. In this work, we develop an approach for characterizing generic attributes of phase transitions from very limited observations made deep within different phases' domains of stability. Our approach is called Thermodynamic Maps, which combines statistical mechanics and molecular simulations with score-based generative models. Thermodynamic Maps enable learning the temperature dependence of arbitrary thermodynamic observables across a wide range of temperatures. We show its usefulness by calculating phase transition attributes such as melting temperature, temperature-dependent heat capacities, and critical exponents. For instance, we demonstrate the ability of thermodynamic maps to infer the ferromagnetic phase transition of the Ising model, including temperature-dependent heat capacity and critical exponents, despite never having seen samples from the transition region. In addition, we efficiently characterize the temperature-dependent conformational ensemble and compute melting curves of the two RNA systems GCAA tetraloop and HIV-TAR, which are notoriously hard to sample due to glassy-like landscapes. © 2023, CC BY.

关键词： Specific heat

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An Information Bottleneck Approach for Markov Model Construction

arXiv

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arXiv 2024年

作者： Wang, Dedi Qiu, Yunrui Beyerle, Eric R. Huang, Xuhui Tiwary, Pratyush Biophysics Program Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Department of Chemistry Theoretical Chemistry Institute University of Wisconsin-Madison MadisonWI53706 United States Data Science Institute University of Wisconsin-Madison MadisonWI53706 United States Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States Department of Chemistry and Biochemistry Institute for Physical Science and Technology University of Maryland College ParkMD20742 United States University of Maryland Institute for Health Computing BethesdaMD20852 United States

Markov state models (MSMs) have proven valuable in studying dynamics of protein conformational changes via statistical analysis of molecular dynamics (MD) simulations. In MSMs, the complex configuration space is coarse-grained into conformational states, with dynamics modeled by a series of Markovian transitions among these states at discrete lag times. Constructing the Markovian model at a specific lag time necessitates defining states that circumvent significant internal energy barriers, enabling internal dynamics relaxation within the lag time. This process effectively coarse-grains time and space, integrating out rapid motions within metastable states. Thus, MSMs possess a multi-resolution nature, where the granularity of states can be adjusted according to the time-resolution, offering flexibility in capturing system dynamics. This work introduces a continuous embedding approach for molecular conformations using the state predictive information bottleneck (SPIB), a framework that unifies dimensionality reduction and state space partitioning via a continuous, machine learned basis set. Without explicit optimization of the VAMP-based scores, SPIB demonstrates state-of-the-art performance in identifying slow dynamical processes and constructing predictive multi-resolution Markovian models. Through applications to well-validated mini-proteins, SPIB showcases unique advantages compared to competing methods. It autonomously and self-consistently adjusts the number of metastable states based on specified minimal time resolution, eliminating the need for manual tuning. While maintaining efficacy in dynamical properties, SPIB excels in accurately distinguishing metastable states and capturing numerous well-populated macrostates. This contrasts with existing VAMP-based methods, which often emphasize slow dynamics at the expense of incorporating numerous sparsely populated states. Furthermore, SPIB’s ability to learn a low-dimensional continuous embedding of the underlyin

关键词： Embeddings

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Alkyl-thiophene-alkyl linkers to construct double-cable conjugated polymers for single-component organic solar cells

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Chinese Chemical Letters 2024年第1期35卷 542-546页

作者： Wenbin Lai Safakath Karuthedath Chengyi Xiao Lei Meng Frédéric Laquai Weiwei Li Yongfang Li Beijing National Laboratory for Molecular Sciences Key Laboratory of Organic SolidsInstitute of ChemistryChinese Academy of SciencesBeijing 100190China Beijing Advanced Innovation Center for Soft Matter Science and Engineering&State Key Laboratory of Organic-Inorganic Composites Beijing University of Chemical TechnologyBeijing 100029China King Abdullah University of Science and Technology(KAUST) KAUST Solar Center(KSC)Physical Sciences and Engineering Division(PSE)Material Science and Engineering Program(MSE)Thuwal 23955-6900Kingdom of Saudi Arabia University of Chinese Academy of Sciences Beijing 100049China Institute of Materials Research Tsinghua Shenzhen International Graduate SchoolTsinghua UniversityShenzhen 518055China

In this work,semirigid linkers of the alkyl-thiophene-alkyl structure are developed to construct double-cable *** alkyl units,propyl(C3H6),hexyl(C6H12),and dodecyl(C12H24),are applied as semirigid linkers,yielding three double-cable polymers:PBC6-T,PBC12-T,and PBC24-T,***12-T which uses C6H12-thiophene-C6H12 linkers is found to exhibit the best device efficiency of 5.56%,while PBC6-T and PBC24-T with shorter or longer linkers yield device efficiencies of only 2.65%and 1.09%in single-component organic solar cells(SCOSCs).Further studies reveal that PBC12-T exhibits higher crystallinity and improved charge transport,resulting in better *** work provides an approach to construct double-cable conjugated polymers with long alkyl linkers,and it shows the importance of the linker length for the photovoltaic performance of SCOSCs.

关键词： Double-cable conjugated polymer Single-component organic solar cell Crystallinity Semirigid linkers Alkyl-thiophene-alkyl

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Effects of Exercise Training on Immune-Related Genes and Pathways in the Cortex of Animal Models of Alzheimer’s Disease: A Systematic Review

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Journal of Alzheimer's Disease 2024年第4期98卷 1219-1234页

作者： Widjaya, Michael Anekson Lee, Shin-Da Cheng, Wei-Chung Wu, Bor-Tsang Graduate Institute of Biomedical Sciences College of Medicine China Medical University Taichung Taiwan Department of Physical Therapy PhD program in Healthcare Science China Medical University Taichung Taiwan Cancer Biology and Precision Therapeutics Center China Medical University Taichung Taiwan Program for Cancer Biology and Drug Discovery China Medical University Academia Sinica Taichung Taiwan Department of Senior Citizen Service Management National Taichung University of Science and Technology Taichung Taiwan

Background: Alzheimer’s disease (AD) is a chronic neurodegenerative disease that affects the immune system due to the accumulation of amyloid-b (Ab) and tau associated molecular pathology and other pathogenic processes. To address AD pathogenesis, various approaches had been conducted from drug development to lifestyle modification to reduce the prevalence of AD. Exercise is considered a prominent lifestyle modification to combat AD. Objective: This observation prompted us to review the literature on exercise related to immune genes in the cortex of animal models of AD. We focused on animal model studies due to their prevalence in this domain. Methods: The systematic review was conducted according to PRISMA standards using Web of science (WoS) and PubMed databases. Any kind of genes, proteins, and molecular molecules were included in this systematic review. The list of these immune-related molecules was analyzed in the STRING database for functional enrichment analysis. Results: We found that 17 research studies discussed immune-related molecules and 30 immune proteins. These studies showed that exercise had the ability to ameliorate dysfunction in AD-related pathways, which led to decreasing the expression of microglia-related pathways and Th17-related immune pathways. As a result of decreasing the expression of immune-related pathways, the expression of apoptosis-related pathways was also decreasing, and neuronal survival was increased by exercise activity. Conclusions: Based on functional enrichment analysis, exercise not only could reduce apoptotic factors and immune components but also could increase cell survival and Ab clearance in cortex samples. PROSPERO ID: CRD42022326093. © 2024 – IOS Press. All rights reserved.

关键词： Alzheimer’s disease apoptosis-related pathway brain microglia-related pathway physical activity Th17-related pathway

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Tungsten Nitride (W5N6): An Ultraresilient 2D Semimetal

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Nano Letters 2024年第1期24卷 67-73页

作者： Chin, Hao-Ting Wang, Deng-Chi Gulo, Desman Perdamaian Yao, Yu-Chi Yeh, Hao-Chen Muthu, Jeyavelan Chen, Ding-Rui Kao, Tzu-Chun Kalbáč, Martin Lin, Ping-Hui Cheng, Cheng-Maw Hofmann, Mario Liang, Chi-Te Liu, Hsiang-Lin Chuang, Feng-Chuan Hsieh, Ya-Ping Molecular Science and Technology Program Taiwan International Graduate Program Academia Sinica Taipei10617 Taiwan International Graduate Program of Molecular Science and Technology National Taiwan University Taipei10617 Taiwan Institute of Atomic and Molecular Sciences Academia Sinica Taipei10617 Taiwan Department of Physics National Sun Yat-Sen University Kaohsiung80424 Taiwan Department of Physics National Taiwan Normal University Taipei11677 Taiwan Department of Physics National Taiwan University Taipei10617 Taiwan Institute of Physics Academia Sinica Taipei115201 Taiwan International Graduate Program of Nano Science and Technology National Taiwan University Taipei10617 Taiwan Graduate Institute of Applied Physics National Taiwan University Taipei10617 Taiwan J. Heyrovský Institute of Physical Chemistry Czech Academy of Sciences Dolejškova 2155/3 Prague182 23 Czech Republic Hsinchu300092 Taiwan Physics Division National Center for Theoretical Sciences Taipei10617 Taiwan Center for Theoretical and Computational Physics National Sun Yat-sen University Kaohsiung80424 Taiwan

Two-dimensional transition metal nitrides offer intriguing possibilities for achieving novel electronic and mechanical functionality owing to their distinctive and tunable bonding characteristics compared to other 2D materials. We demonstrate here the enabling effects of strong bonding on the morphology and functionality of 2D tungsten nitrides. The employed bottom-up synthesis experienced a unique substrate stabilization effect beyond van-der-Waals epitaxy that favored W5N6 over lower metal nitrides. Comprehensive structural and electronic characterization reveals that monolayer W5N6 can be synthesized at large scale and shows semimetallic behavior with an intriguing indirect band structure. Moreover, the material exhibits exceptional resilience against mechanical damage and chemical reactions. Leveraging these electronic properties and robustness, we demonstrate the application of W5N6 as atomic-scale dry etch stops that allow the integration of high-performance 2D materials contacts. These findings highlight the potential of 2D transition metal nitrides for realizing advanced electronic devices and functional interfaces. © 2023 American Chemical Society

关键词： Tungsten compounds

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Three-dimensional magnetization reconstruction from electron optical phase images with physical constraints

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science China(Physics,Mechanics & Astronomy) 2024年第11期67卷 122-132页

作者： Boyao Lyu Shihua Zhao Yibo Zhang Weiwei Wang Fengshan Zheng Rafal E.Dunin-Borkowski Jiadong Zang Haifeng Du Anhui Province Key Laboratory of Low-Energy Quantum Materials and Devices High Magnetic Field LaboratoryHefei Institutes of Physical ScienceChinese Academy of SciencesHefei 230031China Science Island Branch Graduate School of University of Science and Technology of ChinaHefei 230026China Department of Physics and Astronomy University of New HampshireDurham 03824USA Department of Physics The City College of New YorkNew York 10031USA Physics Program Graduate Center of the City University of New YorkNew York 10016USA Department of Chemistry University of New HampshireDurham 03824USA Institutes of Physical Science and Information Technology Anhui UniversityHefei 230601China Spin-X Institute Center for Electron MicroscopySchool of Physics and OptoelectronicsState Key Laboratory of Luminescent Materials and DevicesGuangdong-Hong Kong-Macao Joint Laboratory of Optoelectronic and Magnetic Functional MaterialsSouth China University of TechnologyGuangzhou 511442China Ernst Ruska-Centre for Microscopy and Spectroscopy with Electrons Forschungszentrum JülichJülich 52425Germany

The ability to characterize three-dimensional(3D)magnetization distributions in nanoscale magnetic materials and devices is essential to fully understand their static and dynamic magnetic *** contrast techniques in the transmission electron microscope(TEM),such as electron holography and electron ptychography,can be used to record two-dimensional(2D)projections of the in-plane magnetic induction of 3D nanoscale *** the 3D magnetic induction can in principle be reconstructed from one or more tilt series of such 2D projections,conventional tomographic reconstruction algorithms do not recover the 3D magnetization within a sample ***,we use simulations to describe the basis of an improved model-based algorithm for the tomographic reconstruction of a 3D magnetization distribution from one or more tilt series of electron optical phase images recorded in the *** algorithm allows a wide range of physical constraints,including a priori information about the sample geometry and magnetic parameters,to be *** also makes use of minimization of the micromagnetic energy in the loss *** demonstrate the reconstruction of the 3D magnetization of a localized magnetic soliton—a hopfion ring—and discuss the influence of noise,choice of magnetic constants,maximum tilt angle and number of tilt axes on the *** algorithm can in principle be adapted for other magnetic contrast imaging techniques in the TEM,as well as for other magnetic characterization techniques,such as those based on X-rays or neutrons.

关键词： three-dimensional magnetization vector field tomography differentiable programming electron holography micromagnetism

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Quantifying Energetic and Entropic Pathways in Molecular Systems

arXiv

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arXiv 2022年

作者： Beyerle, E.R. Mehdi, Shams Tiwary, Pratyush Institute for Physical Science and Technology University of Maryland College ParkMD20740 United States Biophysics Program and Institute for Physical Science and Technology University of Maryland College Park20742 United States Department of Chemistry and Biochemistry Institute for Physical Science and Technology University of Maryland College Park20742 United States

When examining dynamics occurring at non-zero temperatures, both energy and entropy must be taken into account while describing activated barrier crossing events. Furthermore, good reaction coordinates need to be constructed to describe different metastable states and the transition mechanisms between them. Here we use a physics-based machine learning method called the State Predictive Information Bottleneck (SPIB) to find non-linear reaction coordinates for three systems of varying complexity. The SPIB is able to predict correctly an entropic bottleneck for an analytical at-energy double-well system and identify the entropyand energy-dominated pathways for an analytical four-well system. Finally, for a simulation of benzoic acid permeation through a lipid bilayer, SPIB is able to discover the the entropic and energetic barriers to the permeation process. Given these results, we thus establish that SPIB is a reasonable and robust method for finding the important entropy and energy/enthalpy barriers in physical systems, which can then be used for enhanced understanding and sampling of different activated mechanisms. © 2022, CC BY.

关键词： Lipid bilayers

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