Physical review research最新文献

Lyapunov theory demonstrating a fundamental limit on the speed of systems consolidation. 李亚普诺夫理论证明了系统整合速度的基本限制。

IF 4.2

Physical review research Pub Date : 2025-04-01 Epub Date: 2025-05-21 DOI: 10.1103/physrevresearch.7.023174

Alireza Alemi, Emre R F Aksay, Mark S Goldman

{"title":"Lyapunov theory demonstrating a fundamental limit on the speed of systems consolidation.","authors":"Alireza Alemi, Emre R F Aksay, Mark S Goldman","doi":"10.1103/physrevresearch.7.023174","DOIUrl":"10.1103/physrevresearch.7.023174","url":null,"abstract":"The nervous system reorganizes memories from an early site to a late site, a commonly observed feature of learning and memory systems known as systems consolidation. Previous work has suggested learning rules by which consolidation may occur. Here, we provide conditions under which such rules are guaranteed to lead to stable convergence of learning and consolidation. We use the theory of Lyapunov functions, which enforces stability by requiring learning rules to decrease an energy-like (Lyapunov) function. We present the theory in the context of a simple circuit architecture motivated by classic models of cerebellum-mediated learning and consolidation. Stability is only guaranteed if the learning rate in the late stage is not faster than the learning rate in the early stage. Further, the slower the learning rate at the late stage, the larger the perturbation the system can tolerate with a guarantee of stability. We provide intuition for this result by mapping a simple example consolidation model to a damped driven oscillator system and showing that the ratio of early- to late-stage learning rates in the consolidation model can be directly identified with the oscillator's damping ratio. We then apply the theory to modeling the tuning by the cerebellum of a well-characterized analog short-term memory system, the oculomotor neural integrator, and find similar stability conditions. This work suggests the power of the Lyapunov approach to provide constraints on nervous system function.","PeriodicalId":520315,"journal":{"name":"Physical review research","volume":"7 2","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12392100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985697","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Symmetry, gauge freedoms, and the interpretability of sequence-function relationships. 对称，规范自由，和序列-函数关系的可解释性。

IF 4.2

Physical review research Pub Date : 2025-04-01 Epub Date: 2025-04-02 DOI: 10.1103/physrevresearch.7.023005

Anna Posfai, David M McCandlish, Justin B Kinney

{"title":"Symmetry, gauge freedoms, and the interpretability of sequence-function relationships.","authors":"Anna Posfai, David M McCandlish, Justin B Kinney","doi":"10.1103/physrevresearch.7.023005","DOIUrl":"https://doi.org/10.1103/physrevresearch.7.023005","url":null,"abstract":"Quantitative models that describe how biological sequences encode functional activities are ubiquitous in modern biology. One important aspect of these models is that they commonly exhibit gauge freedoms, i.e., directions in parameter space that do not affect model predictions. In physics, gauge freedoms arise when physical theories are formulated in ways that respect fundamental symmetries. However, the connections that gauge freedoms in models of sequence-function relationships have to the symmetries of sequence space have yet to be systematically studied. Here we study the gauge freedoms of models that respect a specific symmetry of sequence space: the group of position-specific character permutations. We find that gauge freedoms arise when model parameters transform under redundant irreducible matrix representations of this group. Based on this finding, we describe an \"embedding distillation\" procedure that enables analytic calculation of the number of independent gauge freedoms, as well as efficient computation of a sparse basis for the space of gauge freedoms. We also study how parameter transformation behavior affects parameter interpretability. We find that in many (and possibly all) nontrivial models, the ability to interpret individual model parameters as quantifying intrinsic allelic effects requires that gauge freedoms be present. This finding establishes an incompatibility between two distinct notions of parameter interpretability. Our work thus advances the understanding of symmetries, gauge freedoms, and parameter interpretability in sequence-function relationships.","PeriodicalId":520315,"journal":{"name":"Physical review research","volume":"7 2","pages":""},"PeriodicalIF":4.2,"publicationDate":"2025-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12363380/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144985627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Impact of microwave phase noise on diamond quantum sensing. 微波相位噪声对金刚石量子传感的影响。

IF 4.2

Physical review research Pub Date : 2024-11-01 Epub Date: 2024-11-15 DOI: 10.1103/physrevresearch.6.043148

Andris Berzins, Maziar Saleh Ziabari, Yaser Silani, Ilja Fescenko, Joshua T Damron, John F Barry, Andrey Jarmola, Pauli Kehayias, Bryan A Richards, Janis Smits, Victor M Acosta

{"title":"Impact of microwave phase noise on diamond quantum sensing.","authors":"Andris Berzins, Maziar Saleh Ziabari, Yaser Silani, Ilja Fescenko, Joshua T Damron, John F Barry, Andrey Jarmola, Pauli Kehayias, Bryan A Richards, Janis Smits, Victor M Acosta","doi":"10.1103/physrevresearch.6.043148","DOIUrl":"10.1103/physrevresearch.6.043148","url":null,"abstract":"Precision optical measurements of the electron-spin precession of nitrogen-vacancy (NV) centers in diamond form the basis of numerous applications. The most sensitivity-demanding applications, such as femtotesla magnetometry, require the ability to measure changes in GHz spin transition frequencies at the sub-millihertz level, corresponding to a fractional resolution of better than 10-12. Here we study the impact of microwave (MW) phase noise on the response of an NV sensor. Fluctuations of the phase of the MW waveform cause undesired rotations of the NV spin state. These fluctuations are imprinted in the optical readout signal and, left unmitigated, are indistinguishable from magnetic-field noise. We show that the phase noise of several common commercial MW generators results in an effective <math><mtext>pT</mtext> <mspace></mspace> <msup><mrow><mtext>s</mtext></mrow> <mrow><mn>1</mn> <mo>/</mo> <mn>2</mn></mrow> </msup> </math> -range noise floor that varies with the MW carrier frequency and the detection frequency of the pulse sequence. The data are described by a frequency-domain model incorporating the MW phase-noise spectrum and the filter-function response of the sensing protocol. For controlled injection of white and random-walk phase noise, the observed NV magnetic noise floor is described by simple analytic expressions that accurately capture the scaling with pulse sequence length and the number of <math><mi>π</mi></math> pulses. We outline several strategies to suppress the impact of MW phase noise and implement a version, based on gradiometry, that realizes a > 10-fold suppression. Our study highlights an important challenge in the pursuit of sensitive diamond quantum sensors and is applicable to other qubit systems with a large transition frequency.","PeriodicalId":520315,"journal":{"name":"Physical review research","volume":"6 4","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12524190/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145310577","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Price of information in games of chance: A statistical physics approach. 机会博弈中的信息价格：统计物理方法。

Physical review research Pub Date : 2024-09-04 DOI: 10.1103/PhysRevResearch.6.033250

Luca Gamberi, Alessia Annibale, Pierpaolo Vivo

{"title":"Price of information in games of chance: A statistical physics approach.","authors":"Luca Gamberi, Alessia Annibale, Pierpaolo Vivo","doi":"10.1103/PhysRevResearch.6.033250","DOIUrl":"https://doi.org/10.1103/PhysRevResearch.6.033250","url":null,"abstract":"Information in the form of data, which can be stored and transferred between users, can be viewed as an intangible commodity, which can be traded in exchange for money. Determining the fair price at which a string of data should be traded is an important and open problem in many settings. In this work we develop a statistical physics framework that allows one to determine analytically the fair price of information exchanged between players in a game of chance. For definiteness, we consider a game where N players bet on the binary outcome of a stochastic process and share the entry fees pot if successful. We assume that one player holds information about past outcomes of the game, which they may either use exclusively to improve their betting strategy or offer to sell to another player. We find a sharp transition as the number of players N is tuned across a critical value, between a phase where the transaction is always profitable for the seller and one where it may not be. In both phases, different regimes are possible, depending on the \"quality\" of information being put up for sale: we observe symbiotic regimes, where both parties collude effectively to rig the game in their favor, competitive regimes, where the transaction is unappealing to the data holder as it overly favors a competitor for scarce resources, and even prey-predator regimes, where an exploitative data holder could be giving away bad-quality data to undercut a competitor. Our analytical framework can be generalized to more complex settings and constitutes a flexible tool to address the rich and timely problem of pricing information in games of chance.","PeriodicalId":520315,"journal":{"name":"Physical review research","volume":"6 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-09-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7616869/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142776296","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Holographic-(V)AE: An end-to-end SO(3)-equivariant (variational) autoencoder in Fourier space. 全息-(V)AE：傅里叶空间中端到端SO(3)-等变（变分）自编码器。

Physical review research Pub Date : 2024-04-01 DOI: 10.1103/physrevresearch.6.023006

Gian Marco Visani, Michael N Pun, Arman Angaji, Armita Nourmohammad

{"title":"Holographic-(V)AE: An end-to-end SO(3)-equivariant (variational) autoencoder in Fourier space.","authors":"Gian Marco Visani, Michael N Pun, Arman Angaji, Armita Nourmohammad","doi":"10.1103/physrevresearch.6.023006","DOIUrl":"10.1103/physrevresearch.6.023006","url":null,"abstract":"Group-equivariant neural networks have emerged as an efficient approach to model complex data, using generalized convolutions that respect the relevant symmetries of a system. These techniques have made advances in both the supervised learning tasks for classification and regression, and the unsupervised tasks to generate new data. However, little work has been done in leveraging the symmetry-aware expressive representations that could be extracted from these approaches. Here, we present holographic-(variational) autoencoder [H-(V)AE], a fully end-to-end SO(3)-equivariant (variational) autoencoder in Fourier space, suitable for unsupervised learning and generation of data distributed around a specified origin in 3D. H-(V)AE is trained to reconstruct the spherical Fourier encoding of data, learning in the process a low-dimensional representation of the data (i.e., a latent space) with a maximally informative rotationally invariant embedding alongside an equivariant frame describing the orientation of the data. We extensively test the performance of H-(V)AE on diverse datasets. We show that the learned latent space efficiently encodes the categorical features of spherical images. Moreover, the low-dimensional representations learned by H-VAE can be used for downstream data-scarce tasks. Specifically, we show that H-(V)AE's latent space can be used to extract compact embeddings for protein structure microenvironments, and when paired with a random forest regressor, it enables state-of-the-art predictions of protein-ligand binding affinity.","PeriodicalId":520315,"journal":{"name":"Physical review research","volume":"6 2","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-04-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11661850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142879570","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0