Physical review. E最新文献

{"title":"Second-order mean-field approximation for calculating dynamics in Au-nanoparticle networks","authors":"Evan Wonisch, Jonas Mensing, Andreas Heuer","doi":"10.1103/physreve.110.034103","DOIUrl":"https://doi.org/10.1103/physreve.110.034103","url":null,"abstract":"Exploiting physical processes for fast and energy-efficient computation bears great potential in the advancement of modern hardware components. This paper explores nonlinear charge tunneling in nanoparticle networks, controlled by external voltages. The dynamics are described by a master equation, which expresses the time-evolution of a distribution function over the set of charge occupation numbers. The driving force behind this evolution is charge tunneling events among nanoparticles and their associated rates. We introduce two mean-field approximations to this master equation. By parametrization of the distribution function using its first- and second-order statistical moments, and a subsequent projection of the dynamics onto the resulting moment manifold, one can deterministically calculate expected charges and currents. Unlike a kinetic Monte Carlo approach, which extracts samples from the distribution function, this mean-field approach avoids any random elements. A comparison of results between the mean-field approximation and an already available kinetic Monte Carlo simulation demonstrates great accuracy. Our analysis also reveals that transitioning from a first-order to a second-order approximation significantly enhances the accuracy. Furthermore, we demonstrate the applicability of our approach to time-dependent simulations, using Eulerian time-integration schemes.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"15 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamics of waste proteins in brain tissue: Numerical insights into Alzheimer's risk factors","authors":"Lily Watkins, Saikat Mukherjee, Jeffrey Tithof","doi":"10.1103/physreve.110.034401","DOIUrl":"https://doi.org/10.1103/physreve.110.034401","url":null,"abstract":"Over the past few decades, research has indicated that the buildup of waste proteins, like amyloid-<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mi>β</mi></math> (<math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi mathvariant=\"normal\">A</mi><mi>β</mi></mrow></math>), in the brain's interstitial spaces is linked to neurodegenerative diseases like Alzheimer's, but the details of how such proteins are removed from the brain are not well understood. We have developed a numerical model to investigate the aggregation and clearance mechanisms of <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi mathvariant=\"normal\">A</mi><mi>β</mi></mrow></math> in the interstitial spaces of the brain. The model describes the volume-averaged transport of <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi mathvariant=\"normal\">A</mi><mi>β</mi></mrow></math> in a segment of the brain interstitium modeled as a porous medium, oriented between the perivascular space (fluid-filled channel surrounding a blood vessel) of a penetrating arteriole and that of a venule. Our numerical approach solves <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mi>N</mi></math> coupled advection-diffusion-aggregation equations that model the production, aggregation, fragmentation, and clearance of <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mi>N</mi></math> species of <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi mathvariant=\"normal\">A</mi><mi>β</mi></mrow></math>. We simulate <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi>N</mi><mo>=</mo><mn>50</mn></mrow></math> species to investigate the oligomer-size dependence of clearance and aggregation. We introduce a timescale plot that helps predict <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi mathvariant=\"normal\">A</mi><mi>β</mi></mrow></math> buildup for different neurological conditions. We show that a sudden increase in monomer concentration, as occurs in conditions like traumatic brain injury, leads to significant plaque formation, which can qualitatively be predicted using the timescale plot. Our results also indicate that impaired protein clearance (as occurs with aging) and fragmentation are both mechanisms that sustain large intermediate oligomer concentrations. Our results provide novel insight into several known risk factors for Alzheimer's disease and cognitive decline, and we introduce a unique framing of <math xmlns=\"http://www.w3.org/1998/Math/MathML\"><mrow><mi mathvariant=\"normal\">A</mi><mi>β</mi></mrow></math> dynamics as a competition between different timescales associated with production rates, aggregation rates, and clearance conditions.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"17 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201098","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Ionic current blockade in a nanopore due to an ellipsoidal particle","authors":"Dmitriy V. Melnikov, Nelson R. Barker, Maria E. Gracheva","doi":"10.1103/physreve.110.034403","DOIUrl":"https://doi.org/10.1103/physreve.110.034403","url":null,"abstract":"Nanopores in solid-state membranes have been used to detect, identify, filter, and characterize nanoparticles and biological molecules. In this work, we simulate an ionic flow through a nanopore while an ellipsoidal nanoparticle translocates through a pore. We numerically solve the Poisson-Nernst-Planck equations to obtain the ionic current values for different aspect ratios, sizes, and orientations of a translocating particle. By extending the existing theoretical model for the ionic current in the nanopore to the particles of ellipsoidal shape, we propose semiempirical fitting formulas which describe our computed data within 5% accuracy. We also demonstrate how the derived formulas can be used to identify the dimensions of nanoparticles from the available experimental data which may have useful applications in bionanotechnology.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"17 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Efficiency bounds for bipartite information-thermodynamic systems","authors":"Shihao Xia, Shuanglong Han, Ousi Pan, Yuzhuo Pan, Jincan Chen, Shanhe Su","doi":"10.1103/physreve.110.034102","DOIUrl":"https://doi.org/10.1103/physreve.110.034102","url":null,"abstract":"In this paper, we introduce an approach to derive a lower bound for the entropy production rate of a subsystem by utilizing the Cauchy-Schwarz inequality. It extends to establishing comprehensive upper and lower bounds for the efficiency of two subsystems. These bounds are applicable to a wide range of Markovian stochastic processes, which enhances the accuracy in depicting the range of energy conversion efficiency between subsystems. Empirical validation is conducted using a two-quantum-dot system model, which serves to confirm the effectiveness of our inequality in refining the boundaries of efficiency.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"1 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201087","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Sum rule for fluctuations of work","authors":"Hyogeon Park, Yong Woon Kim, Juyeon Yi","doi":"10.1103/physreve.110.034108","DOIUrl":"https://doi.org/10.1103/physreve.110.034108","url":null,"abstract":"We study the fluctuations of work caused by applying cyclic perturbations and obtain an exact sum rule satisfied by the moments of work for a broad class of quantum stationary ensembles. In the case of the canonical ensemble, the sum rule reproduces the Jarzynski equality. The sum rule can also be simplified into a linear relationship between the work average and the second moment of work, which we numerically confirm via an exact diagonalization of a spin model system.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"17 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201093","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Otto cycles with a quantum planar rotor","authors":"Michael Gaida, Stefan Nimmrichter","doi":"10.1103/physreve.110.034109","DOIUrl":"https://doi.org/10.1103/physreve.110.034109","url":null,"abstract":"We present two realizations of an Otto cycle with a quantum planar rotor as the working medium controlled by means of external fields. By comparing the quantum and the classical description of the working medium, we single out genuine quantum effects with regard to the performance and the engine and refrigerator modes of the Otto cycle. The first example is a rotating electric dipole subjected to a controlled electric field, equivalent to a quantum pendulum. Here we find a systematic disadvantage of the quantum rotor compared to its classical counterpart. In contrast, a genuine quantum advantage can be observed with a charged rotor generating a magnetic moment that is subjected to a controlled magnetic field. We prove that the classical rotor is inoperable as a working medium for any choice of parameters, whereas the quantum rotor supports an engine and a refrigerator mode, exploiting the quantum statistics during the cold strokes of the cycle.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"47 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"How the zebra got its stripes: Curvature-dependent diffusion orients Turing patterns on three-dimensional surfaces","authors":"Michael F. Staddon","doi":"10.1103/physreve.110.034402","DOIUrl":"https://doi.org/10.1103/physreve.110.034402","url":null,"abstract":"Many animals have patterned fur, feathers, or scales, such as the stripes of a zebra. Turing models, or reaction-diffusion systems, are a class of mathematical models of interacting species that have been successfully used to generate animal-like patterns for many species. When diffusion of the inhibitor is high enough relative to the activator, a diffusion-driven instability can spontaneously form patterns. However, it is not just the type of pattern but also the orientation that matters, and it remains unclear how patterns are oriented in practice. Here, we propose a mechanism by which the curvature of the surface influences the rate of diffusion, and can recapture the correct orientation of stripes on models of a zebra and of a cat in numerical simulations. Previous work has shown how anisotropic diffusion can give stripe forming reaction-diffusion systems a bias in orientation. From the observation that zebra stripes run around the direction of highest curvature, that is around the torso and legs, we apply this result by modifying the anisotropic diffusion rates based on the local curvature. These results show how local geometry can influence the reaction dynamics to give robust, global-scale patterns. Overall, this model proposes a coupling between the system geometry and reaction-diffusion dynamics that can give global control over the patterning by using only local curvature information. Such a model can give shape and positioning information in animal development without the need for spatially dependent morphogen gradients.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"44 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201127","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Engineering ratchet-based particle separation via extended shortcuts to isothermality","authors":"Xiu-Hua Zhao, Z. C. Tu, Yu-Han Ma","doi":"10.1103/physreve.110.034105","DOIUrl":"https://doi.org/10.1103/physreve.110.034105","url":null,"abstract":"Microscopic particle separation plays a vital role in various scientific and industrial domains. Conventional separation methods relying on external forces or physical barriers inherently exhibit limitations in terms of efficiency, selectivity, and adaptability across diverse particle types. To overcome these limitations, researchers are constantly exploring new separation approaches, among which ratchet-based separation is a noteworthy method. However, in contrast to the extensive numerical studies and experimental investigations on ratchet separation, its theoretical exploration appears weak, particularly lacking in the analysis of energy consumption involved in the separation processes. The latter is of significant importance for achieving energetically efficient separation. In this paper, we propose a nonequilibrium thermodynamic approach, extending the concept of shortcuts to isothermality, to realize controllable separation of overdamped Brownian particles with low energy cost. By utilizing a designed ratchet potential with temporal period &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;mi&gt;τ&lt;/mi&gt;&lt;/math&gt;, we find in the slow-driving regime that the average particle velocity &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;mrow&gt;&lt;msub&gt;&lt;mover accent=\"true\"&gt;&lt;mi&gt;v&lt;/mi&gt;&lt;mo&gt;¯&lt;/mo&gt;&lt;/mover&gt;&lt;mi&gt;s&lt;/mi&gt;&lt;/msub&gt;&lt;mo&gt;∝&lt;/mo&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;mo&gt;−&lt;/mo&gt;&lt;mi&gt;D&lt;/mi&gt;&lt;mo&gt;/&lt;/mo&gt;&lt;msup&gt;&lt;mi&gt;D&lt;/mi&gt;&lt;mo&gt;*&lt;/mo&gt;&lt;/msup&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;msup&gt;&lt;mi&gt;τ&lt;/mi&gt;&lt;mrow&gt;&lt;mo&gt;−&lt;/mo&gt;&lt;mn&gt;1&lt;/mn&gt;&lt;/mrow&gt;&lt;/msup&gt;&lt;/mrow&gt;&lt;/math&gt;, indicating that particles with different diffusion coefficients &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;mi&gt;D&lt;/mi&gt;&lt;/math&gt; can be guided to move in distinct directions with a preset &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;msup&gt;&lt;mi&gt;D&lt;/mi&gt;&lt;mo&gt;*&lt;/mo&gt;&lt;/msup&gt;&lt;/math&gt;. It is revealed that an inevitable portion of the energy cost in separation depends on the driving dynamics of the ratchet, with an achievable lower bound &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;mrow&gt;&lt;msubsup&gt;&lt;mi&gt;W&lt;/mi&gt;&lt;mrow&gt;&lt;mi&gt;ex&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;mi&gt;min&lt;/mi&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/msubsup&gt;&lt;mo&gt;∝&lt;/mo&gt;&lt;msup&gt;&lt;mi mathvariant=\"script\"&gt;L&lt;/mi&gt;&lt;mn&gt;2&lt;/mn&gt;&lt;/msup&gt;&lt;mrow&gt;&lt;mo&gt;|&lt;/mo&gt;&lt;msub&gt;&lt;mover accent=\"true\"&gt;&lt;mi&gt;v&lt;/mi&gt;&lt;mo&gt;¯&lt;/mo&gt;&lt;/mover&gt;&lt;mi&gt;s&lt;/mi&gt;&lt;/msub&gt;&lt;mo&gt;|&lt;/mo&gt;&lt;/mrow&gt;&lt;/mrow&gt;&lt;/math&gt;. Here, &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;mi mathvariant=\"script\"&gt;L&lt;/mi&gt;&lt;/math&gt; is the thermodynamic length of the driving loop in the parametric space. With a sawtooth potential, we numerically test the theoretical findings and illustrate the optimal separation protocol associated with &lt;math xmlns=\"http://www.w3.org/1998/Math/MathML\"&gt;&lt;msubsup&gt;&lt;mi&gt;W&lt;/mi&gt;&lt;mrow&gt;&lt;mi&gt;ex&lt;/mi&gt;&lt;/mrow&gt;&lt;mrow&gt;&lt;mo&gt;(&lt;/mo&gt;&lt;mi&gt;min&lt;/mi&gt;&lt;mo&gt;)&lt;/mo&gt;&lt;/mrow&gt;&lt;/msubsup&gt;&lt;/math&gt;. Finally, for practical considerations, we compare our approach with the conventional ratchets in terms of separation velocity and energy consumption. The scalability of the current framework for separating various particles in two-dimensional space is al","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"728 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201091","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Desensitization to commodity price fluctuations by product characteristics","authors":"Keiji Sakakibara, Daniel M. Packwood","doi":"10.1103/physreve.110.034106","DOIUrl":"https://doi.org/10.1103/physreve.110.034106","url":null,"abstract":"Little is known about how commodity price fluctuations transmit to the prices of products. In this paper we present a price dynamics model for a product which is in competition with a commodity. The price of the commodity is treated as a stochastic process. Commodity price fluctuations are transmitted to the product price through a demand function which is obtained by aggregating the choices of a consumer population. Importantly, these consumers make their choices on the basis of a utility function which includes a term relating to product characteristics. Numerical simulations show that improved product characteristics tend to suppress the transmission of commodity price fluctuations. We apply our model to a realistic case of monolayer platinum (a product) in competition with platinum metal (a commodity) for adoption by consumers as a catalyst material. While monolayer platinum shows only a minor improvement in catalytic turnover rates for oxygen reduction, the resulting product characteristic improvement is sufficient to effectively eliminate product price fluctuations, at least for the consumer population regime considered here.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"8 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201099","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exact solutions for a coherent phenomenon of condensation in conservative Hamiltonian systems","authors":"Anxo Biasi","doi":"10.1103/physreve.110.034107","DOIUrl":"https://doi.org/10.1103/physreve.110.034107","url":null,"abstract":"While it is known that Hamiltonian systems may undergo a phenomenon of condensation akin to Bose-Einstein condensation, not all the manifestations of this phenomenon have been uncovered yet. In this work, we present a novel form of condensation in conservative Hamiltonian systems that stands out due to its evolution through highly coherent states. The result is based on a deterministic approach to obtain exact explicit solutions representing the dynamical formation of condensates in finite time. We reveal a dual-cascade behavior during the process, featuring inverse and direct transfer of conserved quantities across the spectrum. The direct cascade yields the excitation of arbitrarily high modes in finite time, being associated with the formation of a small-scale coherent structure. We provide a fully analytic description of the processes involved.","PeriodicalId":20085,"journal":{"name":"Physical review. E","volume":"4 1","pages":""},"PeriodicalIF":2.4,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142201092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"物理与天体物理","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}