Pub Date : 2023-11-14DOI: 10.1103/physrevb.108.184411
Sourabh Manna, Rohit Medwal, Rajdeep Singh Rawat
In this paper, we theoretically investigate neuronlike spiking dynamics in an elliptic ferromagnet (FM)/heavy metal bilayer-based spin Hall nano-oscillator (SHNO) in a bias field free condition, very suitable for practical realization of brain-inspired computing schemes. We demonstrate regular periodic spiking with tunable frequency as well as the leaky integrate-and-fire (LIF) behavior in a single SHNO by manipulating the pulse features of input current. The frequency of regular periodic spiking is tunable in a range of 0.5--0.96 GHz (460 MHz bandwidth) through adjusting the magnitude of constant input DC current density. We further demonstrate the reconfigurability of spiking dynamics in response to a time-varying input accomplished by continuously increasing the input current density as a linear function of time. Macrospin theory and micromagnetic simulation provide insight into the origin of bias field free auto-oscillation and the spiking phenomena in our SHNO. In addition, we discuss how the shape anisotropy of the elliptic FM influence the bias field free auto-oscillation characteristics, including threshold current, frequency, and transition from in-plane to out-of-plane precession. The SHNO operates $<{10}^{12}phantom{rule{0.16em}{0ex}}mathrm{A}/{mathrm{m}}^{2}$ input current density and exhibits a large auto-oscillation amplitude, ensuring high output power. We show that the threshold current density can be reduced by decreasing the ellipticity of the FM layer as well as enhancing the perpendicular magnetic anisotropy. These findings highlight the potential of bias field free elliptic SHNO in designing power-efficient spiking neuron-based neuromorphic hardware.
{"title":"Reconfigurable neural spiking in bias field free spin Hall nano-oscillator","authors":"Sourabh Manna, Rohit Medwal, Rajdeep Singh Rawat","doi":"10.1103/physrevb.108.184411","DOIUrl":"https://doi.org/10.1103/physrevb.108.184411","url":null,"abstract":"In this paper, we theoretically investigate neuronlike spiking dynamics in an elliptic ferromagnet (FM)/heavy metal bilayer-based spin Hall nano-oscillator (SHNO) in a bias field free condition, very suitable for practical realization of brain-inspired computing schemes. We demonstrate regular periodic spiking with tunable frequency as well as the leaky integrate-and-fire (LIF) behavior in a single SHNO by manipulating the pulse features of input current. The frequency of regular periodic spiking is tunable in a range of 0.5--0.96 GHz (460 MHz bandwidth) through adjusting the magnitude of constant input DC current density. We further demonstrate the reconfigurability of spiking dynamics in response to a time-varying input accomplished by continuously increasing the input current density as a linear function of time. Macrospin theory and micromagnetic simulation provide insight into the origin of bias field free auto-oscillation and the spiking phenomena in our SHNO. In addition, we discuss how the shape anisotropy of the elliptic FM influence the bias field free auto-oscillation characteristics, including threshold current, frequency, and transition from in-plane to out-of-plane precession. The SHNO operates $<{10}^{12}phantom{rule{0.16em}{0ex}}mathrm{A}/{mathrm{m}}^{2}$ input current density and exhibits a large auto-oscillation amplitude, ensuring high output power. We show that the threshold current density can be reduced by decreasing the ellipticity of the FM layer as well as enhancing the perpendicular magnetic anisotropy. These findings highlight the potential of bias field free elliptic SHNO in designing power-efficient spiking neuron-based neuromorphic hardware.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"41 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134900662","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreve.108.054408
C. Brandon Ogbunugafor, Rafael F. Guerrero, Miles D. Miller-Dickson, Eugene I. Shakhnovich, Matthew D. Shoulders
Protein space is a rich analogy for genotype-phenotype maps, where amino acid sequence is organized into a high-dimensional space that highlights the connectivity between protein variants. It is a useful abstraction for understanding the process of evolution, and for efforts to engineer proteins towards desirable phenotypes. Few mentions of protein space consider how protein phenotypes can be described in terms of their biophysical components, nor do they rigorously interrogate how forces like epistasis---describing the nonlinear interaction between mutations and their phenotypic consequences---manifest across these components. In this study, we deconstruct a low-dimensional protein space of a bacterial enzyme (dihydrofolate reductase; DHFR) into ``subspaces'' corresponding to a set of kinetic and thermodynamic traits [${k}_{mathrm{cat}}, {K}_{M}, {K}_{i}$, and ${T}_{m}$ (melting temperature)]. We then examine how combinations of three mutations (eight alleles in total) display pleiotropy, or unique effects on individual subspace traits. We examine protein spaces across three orthologous DHFR enzymes (Escherichia coli, Listeria grayi, and Chlamydia muridarum), adding a genotypic context dimension through which epistasis occurs across subspaces. In doing so, we reveal that protein space is a deceptively complex notion, and that future applications to bioengineering should consider how interactions between amino acid substitutions manifest across different phenotypic subspaces.
{"title":"Epistasis and pleiotropy shape biophysical protein subspaces associated with drug resistance","authors":"C. Brandon Ogbunugafor, Rafael F. Guerrero, Miles D. Miller-Dickson, Eugene I. Shakhnovich, Matthew D. Shoulders","doi":"10.1103/physreve.108.054408","DOIUrl":"https://doi.org/10.1103/physreve.108.054408","url":null,"abstract":"Protein space is a rich analogy for genotype-phenotype maps, where amino acid sequence is organized into a high-dimensional space that highlights the connectivity between protein variants. It is a useful abstraction for understanding the process of evolution, and for efforts to engineer proteins towards desirable phenotypes. Few mentions of protein space consider how protein phenotypes can be described in terms of their biophysical components, nor do they rigorously interrogate how forces like epistasis---describing the nonlinear interaction between mutations and their phenotypic consequences---manifest across these components. In this study, we deconstruct a low-dimensional protein space of a bacterial enzyme (dihydrofolate reductase; DHFR) into ``subspaces'' corresponding to a set of kinetic and thermodynamic traits [${k}_{mathrm{cat}}, {K}_{M}, {K}_{i}$, and ${T}_{m}$ (melting temperature)]. We then examine how combinations of three mutations (eight alleles in total) display pleiotropy, or unique effects on individual subspace traits. We examine protein spaces across three orthologous DHFR enzymes (Escherichia coli, Listeria grayi, and Chlamydia muridarum), adding a genotypic context dimension through which epistasis occurs across subspaces. In doing so, we reveal that protein space is a deceptively complex notion, and that future applications to bioengineering should consider how interactions between amino acid substitutions manifest across different phenotypic subspaces.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"42 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134900655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physrevb.108.174505
P. Holmvall, A. M. Black-Schaffer
Chiral superconductors spontaneously break time-reversal symmetry and host topologically protected edge modes, supposedly generating chiral edge currents which are typically taken as a characteristic fingerprint of chiral superconductivity. However, recent studies have shown that the total edge current in two dimensions (2D) often vanishes for all chiral superconductors except for chiral $p$-wave, especially at low temperatures, thus severely impeding potential experimental verification and characterization of these superconductors. In this work, we use the quasiclassical theory of superconductivity to study mesoscopic disk-schaped chiral $d$-wave superconductors. We find that mesoscopic finite-size effects cause a dramatic enhancement of the total charge current and orbital magnetic moment (OMM), even at low temperatures. We study how these quantities scale with temperature, spontaneous Meissner screening, and system radius $mathcal{R}ensuremath{in}[5,200]{ensuremath{xi}}_{0}$ with superconducting coherence length ${ensuremath{xi}}_{0}$. We find a general $1/mathcal{R}$ scaling in the total charge current and OMM for sufficiently large systems, but this breaks down in small systems, instead producing a local maximum at $mathcal{R}ensuremath{approx}10--20{ensuremath{xi}}_{0}$ due to mesoscopic finite-size effects. These effects also cause a spontaneous charge-current reversal opposite to the chirality below $mathcal{R}<10{ensuremath{xi}}_{0}$. Our work highlights mesoscopic systems as a route to experimentally verify chiral $d$-wave superconductivity, measurable with magnetometry.
{"title":"Enhanced chiral edge currents and orbital magnetic moment in chiral d -wave superconductors from mesoscopic finite-size effects","authors":"P. Holmvall, A. M. Black-Schaffer","doi":"10.1103/physrevb.108.174505","DOIUrl":"https://doi.org/10.1103/physrevb.108.174505","url":null,"abstract":"Chiral superconductors spontaneously break time-reversal symmetry and host topologically protected edge modes, supposedly generating chiral edge currents which are typically taken as a characteristic fingerprint of chiral superconductivity. However, recent studies have shown that the total edge current in two dimensions (2D) often vanishes for all chiral superconductors except for chiral $p$-wave, especially at low temperatures, thus severely impeding potential experimental verification and characterization of these superconductors. In this work, we use the quasiclassical theory of superconductivity to study mesoscopic disk-schaped chiral $d$-wave superconductors. We find that mesoscopic finite-size effects cause a dramatic enhancement of the total charge current and orbital magnetic moment (OMM), even at low temperatures. We study how these quantities scale with temperature, spontaneous Meissner screening, and system radius $mathcal{R}ensuremath{in}[5,200]{ensuremath{xi}}_{0}$ with superconducting coherence length ${ensuremath{xi}}_{0}$. We find a general $1/mathcal{R}$ scaling in the total charge current and OMM for sufficiently large systems, but this breaks down in small systems, instead producing a local maximum at $mathcal{R}ensuremath{approx}10--20{ensuremath{xi}}_{0}$ due to mesoscopic finite-size effects. These effects also cause a spontaneous charge-current reversal opposite to the chirality below $mathcal{R}<10{ensuremath{xi}}_{0}$. Our work highlights mesoscopic systems as a route to experimentally verify chiral $d$-wave superconductivity, measurable with magnetometry.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"36 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134954094","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physrevb.108.184201
Longyan Gong
We introduce a family of one-dimensional aperiodic tight-binding models with linearly varying patches of $A$-type sites with on-site energies ${ensuremath{epsilon}}_{A}=0$ connected by single $B$-type sites with ${ensuremath{epsilon}}_{B}=W$. We analytically show such structures have strong spatial correlations. We theoretically find states are extended at resonance levels in the vicinity of ${E}_{M}^{ensuremath{kappa}}=ensuremath{-}2cosfrac{ensuremath{kappa}ensuremath{pi}}{M}$ if they are allowed energies, where $M=md$ are the size differences of patches, $d$ is the variation rate of patch sizes, $mensuremath{in}{mathcal{N}}_{+}$, and $ensuremath{kappa}=1,2,...,Mensuremath{-}1$. Related delocalization-localization transitions are explored. Numerical evidence is in excellent quantitative agreement with theoretical predictions.
{"title":"Extended states in one-dimensional aperiodic lattices with linearly varying patches","authors":"Longyan Gong","doi":"10.1103/physrevb.108.184201","DOIUrl":"https://doi.org/10.1103/physrevb.108.184201","url":null,"abstract":"We introduce a family of one-dimensional aperiodic tight-binding models with linearly varying patches of $A$-type sites with on-site energies ${ensuremath{epsilon}}_{A}=0$ connected by single $B$-type sites with ${ensuremath{epsilon}}_{B}=W$. We analytically show such structures have strong spatial correlations. We theoretically find states are extended at resonance levels in the vicinity of ${E}_{M}^{ensuremath{kappa}}=ensuremath{-}2cosfrac{ensuremath{kappa}ensuremath{pi}}{M}$ if they are allowed energies, where $M=md$ are the size differences of patches, $d$ is the variation rate of patch sizes, $mensuremath{in}{mathcal{N}}_{+}$, and $ensuremath{kappa}=1,2,...,Mensuremath{-}1$. Related delocalization-localization transitions are explored. Numerical evidence is in excellent quantitative agreement with theoretical predictions.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"35 12","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134953950","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreva.108.l051301
Nikolay Yegovtsev, Victor Gurarie
The authors study the effective mass of a heavy impurity moving through a Bose-Einstein condensate, and the condensate-induced attraction between two such impurities in the regime of strong boson-impurity interactions. This problem turns out to be analytically solvable in the regime of small gas densities.
{"title":"Effective mass and interaction energy of heavy Bose polarons at unitarity","authors":"Nikolay Yegovtsev, Victor Gurarie","doi":"10.1103/physreva.108.l051301","DOIUrl":"https://doi.org/10.1103/physreva.108.l051301","url":null,"abstract":"The authors study the effective mass of a heavy impurity moving through a Bose-Einstein condensate, and the condensate-induced attraction between two such impurities in the regime of strong boson-impurity interactions. This problem turns out to be analytically solvable in the regime of small gas densities.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"61 14","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134900905","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreva.108.053507
Alexandr Karpenko, Mikhail Korobko, Sergey P. Vyatchanin
Quantum optomechanical systems enable the study of fundamental questions on the quantum nature of massive objects. For that a strong coupling between light and mechanical motion is required, which presents a challenge for massive objects. In particular, large interferometric sensors with low-frequency oscillators are difficult to bring into the quantum regime. Here we propose unbalancing the central beam splitter in the Michelson-Sagnac interferometer, which allows us to boost the optomechanical coupling strength compared with a balanced beam splitter. This unbalancing allows us to enhance the cooperative action of two types of optomechanical coupling present in the system: dissipative and dispersive. We analyze two different configurations, in which the optomechanical cavity is formed by the mirror for the laser pump field (power recycling) and by the mirror for the signal field (signal recycling). We show that the imbalance of the beam splitter allows us to dramatically increase the optical cooling of the test-mass motion. We also formulate the conditions for observing quantum radiation-pressure noise and ponderomotive squeezing. Our configuration could serve as the basis for more complex modifications of the interferometer that would utilize the enhanced coupling strength. This would allow us to efficiently reach the quantum state of large test masses, opening the way to studying the fundamental aspects of quantum mechanics and the experimental search for quantum gravity.
{"title":"Enhanced optomechanical interaction in an unbalanced Michelson-Sagnac interferometer","authors":"Alexandr Karpenko, Mikhail Korobko, Sergey P. Vyatchanin","doi":"10.1103/physreva.108.053507","DOIUrl":"https://doi.org/10.1103/physreva.108.053507","url":null,"abstract":"Quantum optomechanical systems enable the study of fundamental questions on the quantum nature of massive objects. For that a strong coupling between light and mechanical motion is required, which presents a challenge for massive objects. In particular, large interferometric sensors with low-frequency oscillators are difficult to bring into the quantum regime. Here we propose unbalancing the central beam splitter in the Michelson-Sagnac interferometer, which allows us to boost the optomechanical coupling strength compared with a balanced beam splitter. This unbalancing allows us to enhance the cooperative action of two types of optomechanical coupling present in the system: dissipative and dispersive. We analyze two different configurations, in which the optomechanical cavity is formed by the mirror for the laser pump field (power recycling) and by the mirror for the signal field (signal recycling). We show that the imbalance of the beam splitter allows us to dramatically increase the optical cooling of the test-mass motion. We also formulate the conditions for observing quantum radiation-pressure noise and ponderomotive squeezing. Our configuration could serve as the basis for more complex modifications of the interferometer that would utilize the enhanced coupling strength. This would allow us to efficiently reach the quantum state of large test masses, opening the way to studying the fundamental aspects of quantum mechanics and the experimental search for quantum gravity.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"34 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134901349","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreva.108.053710
Bochao Wei, Chao Li, Ce Pei, Chandra Raman
We demonstrate a key ingredient in a bottom-up approach to building complex quantum matter using thermal atomic vapors. We isolate and track very slowly moving individual atoms without the aid of laser cooling. Passive filtering enables us to carefully select atoms whose three-dimensional velocity vector has a magnitude below $overline{v}/20$, where $overline{v}$ is the mean velocity of the ensemble. Using a photon correlation technique, we can extract the velocity distributions. We can also follow the trajectory of slowly moving single atoms for more than $1phantom{rule{4pt}{0ex}}textmu{}mathrm{s}$ within a $25text{ensuremath{-}}textmu{}mathrm{m}$ field of view, with no obvious limit to the tracking ability while simultaneously observing Rabi oscillations of these single emitters. In addition, we measure the third-order correlation function of single thermal atoms. Our results demonstrate the power and scalability of thermal ensembles for utilization in quantum memories, imaging, and other quantum information applications through bottom-up approaches.
{"title":"Bottom-up approach to room-temperature quantum systems","authors":"Bochao Wei, Chao Li, Ce Pei, Chandra Raman","doi":"10.1103/physreva.108.053710","DOIUrl":"https://doi.org/10.1103/physreva.108.053710","url":null,"abstract":"We demonstrate a key ingredient in a bottom-up approach to building complex quantum matter using thermal atomic vapors. We isolate and track very slowly moving individual atoms without the aid of laser cooling. Passive filtering enables us to carefully select atoms whose three-dimensional velocity vector has a magnitude below $overline{v}/20$, where $overline{v}$ is the mean velocity of the ensemble. Using a photon correlation technique, we can extract the velocity distributions. We can also follow the trajectory of slowly moving single atoms for more than $1phantom{rule{4pt}{0ex}}textmu{}mathrm{s}$ within a $25text{ensuremath{-}}textmu{}mathrm{m}$ field of view, with no obvious limit to the tracking ability while simultaneously observing Rabi oscillations of these single emitters. In addition, we measure the third-order correlation function of single thermal atoms. Our results demonstrate the power and scalability of thermal ensembles for utilization in quantum memories, imaging, and other quantum information applications through bottom-up approaches.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"39 13","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134901629","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreve.108.054407
F. Terragni, W. D. Martinson, M. Carretero, P. K. Maini, L. L. Bonilla
Complex biological processes involve collective behavior of entities (bacteria, cells, animals) over many length and time scales and can be described by discrete models that track individuals or by continuum models involving densities and fields. We consider hybrid stochastic agent-based models of branching morphogenesis and angiogenesis (new blood vessel creation from preexisting vasculature), which treat cells as individuals that are guided by underlying continuous chemical and/or mechanical fields. In these descriptions, leader (tip) cells emerge from existing branches and follower (stalk) cells build the new sprout in their wake. Vessel branching and fusion (anastomosis) occur as a result of tip and stalk cell dynamics. Coarse graining these hybrid models in appropriate limits produces continuum partial differential equations (PDEs) for endothelial cell densities that are more analytically tractable. While these models differ in nonlinearity, they produce similar equations at leading order when chemotaxis is dominant. We analyze this leading order system in a simple quasi-one-dimensional geometry and show that the numerical solution of the leading order PDE is well described by a soliton wave that evolves from vessel to source. This wave is an attractor for intermediate times until it arrives at the hypoxic region releasing the growth factor. The mathematical techniques used here thus identify common features of discrete and continuum approaches and provide insight into general biological mechanisms governing their collective dynamics.
{"title":"Soliton approximation in continuum models of leader-follower behavior","authors":"F. Terragni, W. D. Martinson, M. Carretero, P. K. Maini, L. L. Bonilla","doi":"10.1103/physreve.108.054407","DOIUrl":"https://doi.org/10.1103/physreve.108.054407","url":null,"abstract":"Complex biological processes involve collective behavior of entities (bacteria, cells, animals) over many length and time scales and can be described by discrete models that track individuals or by continuum models involving densities and fields. We consider hybrid stochastic agent-based models of branching morphogenesis and angiogenesis (new blood vessel creation from preexisting vasculature), which treat cells as individuals that are guided by underlying continuous chemical and/or mechanical fields. In these descriptions, leader (tip) cells emerge from existing branches and follower (stalk) cells build the new sprout in their wake. Vessel branching and fusion (anastomosis) occur as a result of tip and stalk cell dynamics. Coarse graining these hybrid models in appropriate limits produces continuum partial differential equations (PDEs) for endothelial cell densities that are more analytically tractable. While these models differ in nonlinearity, they produce similar equations at leading order when chemotaxis is dominant. We analyze this leading order system in a simple quasi-one-dimensional geometry and show that the numerical solution of the leading order PDE is well described by a soliton wave that evolves from vessel to source. This wave is an attractor for intermediate times until it arrives at the hypoxic region releasing the growth factor. The mathematical techniques used here thus identify common features of discrete and continuum approaches and provide insight into general biological mechanisms governing their collective dynamics.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"13 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134991293","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreve.108.054122
Atri Goswami, Utsa Dey, Sudip Mukherjee
We propose and study a one-dimensional (1D) model consisting of two lanes with open boundaries. One of the lanes executes diffusive and the other lane driven unidirectional or asymmetric exclusion dynamics, which are mutually coupled through particle exchanges in the bulk. We elucidate the generic nonuniform steady states in this model. We show that in a parameter regime, where hopping along the TASEP lane, diffusion along the SEP lane, and the exchange of particles between the TASEP and SEP lanes compete, the SEP diffusivity $D$ appears as a tuning parameter for both the SEP and TASEP densities for a given exchange rate in the nonequilibrium steady states of this model. Indeed, $D$ can be tuned to achieve phase coexistence in the asymmetric exclusion dynamics together with spatially smoothly varying density in the diffusive dynamics in the steady state. We obtain phase diagrams of the model using mean field theories, and corroborate and complement the results with stochastic Monte Carlo simulations. This model reduces to an isolated open totally asymmetric exclusion process (TASEP) and an open TASEP with bulk particle nonconserving Langmuir kinetics (LK), respectively, in the limits of vanishing and diverging particle diffusivity in the lane executing diffusive dynamics. Thus, this model works as an overarching general model, connecting both pure TASEPs and TASEPs with LK in different asymptotic limits. We further define phases in the SEP and obtain phase diagrams and show their correspondence with the TASEP phases. In addition to its significance as a 1D driven, diffusive model, this model also serves as a simple reduced model for cell biological transport by molecular motors undergoing diffusive and directed motion inside eukaryotic cells.
{"title":"Nonequilibrium steady states in coupled asymmetric and symmetric exclusion processes","authors":"Atri Goswami, Utsa Dey, Sudip Mukherjee","doi":"10.1103/physreve.108.054122","DOIUrl":"https://doi.org/10.1103/physreve.108.054122","url":null,"abstract":"We propose and study a one-dimensional (1D) model consisting of two lanes with open boundaries. One of the lanes executes diffusive and the other lane driven unidirectional or asymmetric exclusion dynamics, which are mutually coupled through particle exchanges in the bulk. We elucidate the generic nonuniform steady states in this model. We show that in a parameter regime, where hopping along the TASEP lane, diffusion along the SEP lane, and the exchange of particles between the TASEP and SEP lanes compete, the SEP diffusivity $D$ appears as a tuning parameter for both the SEP and TASEP densities for a given exchange rate in the nonequilibrium steady states of this model. Indeed, $D$ can be tuned to achieve phase coexistence in the asymmetric exclusion dynamics together with spatially smoothly varying density in the diffusive dynamics in the steady state. We obtain phase diagrams of the model using mean field theories, and corroborate and complement the results with stochastic Monte Carlo simulations. This model reduces to an isolated open totally asymmetric exclusion process (TASEP) and an open TASEP with bulk particle nonconserving Langmuir kinetics (LK), respectively, in the limits of vanishing and diverging particle diffusivity in the lane executing diffusive dynamics. Thus, this model works as an overarching general model, connecting both pure TASEPs and TASEPs with LK in different asymptotic limits. We further define phases in the SEP and obtain phase diagrams and show their correspondence with the TASEP phases. In addition to its significance as a 1D driven, diffusive model, this model also serves as a simple reduced model for cell biological transport by molecular motors undergoing diffusive and directed motion inside eukaryotic cells.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"42 6","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134900656","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2023-11-14DOI: 10.1103/physreva.108.052212
Martin Plávala, Matthias Kleinmann
We show that the phase-space formulation of general probabilistic theories can be extended to include a generalized time evolution and that it can describe a nonquantum hydrogenlike system which is stable, has discrete energy levels, and includes the Zeeman effect. This allows us to study dynamical effects such as excitations of the hydrogenlike system by a resonant laser and Rutherford scattering. Our construction demonstrates that classical theory and quantum theory can be seen as specific choices of general probabilistic theory in phase space and that other probabilistic theories also lead to measurable predictions.
{"title":"Generalized dynamical theories in phase space and the hydrogen atom","authors":"Martin Plávala, Matthias Kleinmann","doi":"10.1103/physreva.108.052212","DOIUrl":"https://doi.org/10.1103/physreva.108.052212","url":null,"abstract":"We show that the phase-space formulation of general probabilistic theories can be extended to include a generalized time evolution and that it can describe a nonquantum hydrogenlike system which is stable, has discrete energy levels, and includes the Zeeman effect. This allows us to study dynamical effects such as excitations of the hydrogenlike system by a resonant laser and Rutherford scattering. Our construction demonstrates that classical theory and quantum theory can be seen as specific choices of general probabilistic theory in phase space and that other probabilistic theories also lead to measurable predictions.","PeriodicalId":20121,"journal":{"name":"Physical Review","volume":"36 21","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134954089","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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