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BPS2025 - Structural basis of potassium selectivity in kalium channelrhodopsins

Biophysical Journal 2025年第3期124卷 64a-65a页

作者： Seiya Tajima Yoon Seok Kim YoungJu Jo Peter Y. Wang Joseph M. Paggi Charu Ramakrishnan Shunki Takaramoto Takashi Nagata Masae Konno Kota Katayama Hideki Kandori Ron O. Dror Keiichi Inoue Karl Deisseroth Hideaki Kato Research Center for Advanced Science and Technology The University of Tokyo Tokyo Japan Department of Bioengineering Stanford University Stanford CA USA Department of Computer Science Stanford University Stanford CA USA Cracking the Neural Code Program Stanford University Stanford CA USA The Institute for Solid State Physics The University of Tokyo Kashiwa Japan PRESTO Japan Science and Technology Agency Kawaguchi Japan Department of Life Science and Applied Chemistry Nagoya Institute of Technology Nagoya Japan OptoBioTechnology Research Center Nagoya Institute of Technology Nagoya Japan Institute for Computational and Mathematical Engineering Stanford University Stanford CA USA Howard Hughes Medical Institute Stanford University Stanford CA USA Graduate School of Arts and Sciences The University of Tokyo Tokyo Japan

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An integrative systems-biology approach defines mechanisms of Alzheimer’s disease neurodegeneration

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Nature Communications 2025年第1期16卷 1-21页

作者： Leventhal, Matthew J. Zanella, Camila A. Kang, Byunguk Peng, Jiajie Gritsch, David Liao, Zhixiang Bukhari, Hassan Wang, Tao Pao, Ping-Chieh Danquah, Serwah Benetatos, Joseph Nehme, Ralda Farhi, Samouil Tsai, Li-Huei Dong, Xianjun Scherzer, Clemens R. Feany, Mel B. Fraenkel, Ernest MIT Ph.D. Program in Computational and Systems Biology Cambridge MA United States Department of Biological Engineering Massachusetts Institute of Technology Cambridge MA United States Broad Institute of Harvard and MIT Cambridge MA United States Department of Pathology Brigham and Women’s Hospital and Harvard Medical School Boston MA United States Spatial Technology Platform Broad Institute of Harvard and MIT Cambridge MA United States Precision Neurology Program Brigham and Women’s Hospital and Harvard Medical school Boston MA United States APDA Center for Advanced Parkinson’s Disease Research Brigham and Women’s Hospital and Harvard Medical School Boston MA United States Picower Institute for Learning and Memory Massachusetts Institute of Technology Cambridge MA United States Department of Brain and Cognitive Sciences Massachusetts Institute of Technology Cambridge MA United States Stanley Center for Psychiatric Research Broad Institute of Harvard and MIT Cambridge MA United States School of Computer Science Northwestern Polytechnical University Xi’an China Stephen and Denise Adams Center of Yale School of Medicine New Haven CT United States

Despite years of intense investigation, the mechanisms underlying neuronal death in Alzheimer’s disease, remain incompletely understood. To define relevant pathways, we conducted an unbiased, genome-scale forward genetic screen for age-associated neurodegeneration in Drosophila. We also measured proteomics, phosphoproteomics, and metabolomics in Drosophila models of Alzheimer’s disease and identified Alzheimer’s genetic variants that modify gene expression in disease-vulnerable neurons in humans. We then used a network model to integrate these data with previously published Alzheimer’s disease proteomics, lipidomics and genomics. Here, we computationally predict and experimentally confirm how HNRNPA2B1 and MEPCE enhance toxicity of the tau protein, a pathological feature of Alzheimer’s disease. Furthermore, we demonstrated that the screen hits CSNK2A1 and NOTCH1 regulate DNA damage in Drosophila and human stem cell-derived neural progenitor cells. Our study identifies candidate pathways that could be targeted to ameliorate neurodegeneration in Alzheimer’s disease. © The Author(s) 2025.

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Circadian phase entrainment via nonlinear model predictive control

Circadian phase entrainment via nonlinear model predictive c...

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2006 AIChE Annual Meeting

作者： Bagheri, Neda Stelling, Jorg Doyle, III, Francis J. Department of Electrical and Computer Engineering University of California Santa Barbara Santa Barbara CA 93106-5080 United States Department of Chemical Engineering University of California Santa Barbara Santa Barbara CA 93106-5080 United States Biomolecular Science and Engineering Program University of California Santa Barbara Santa Barbara CA 93106-5080 United States Institute of Computational Science ETH Zurich 8092 Zurich Switzerland

No abstract available

ISBN: (纸本)081691012X

No abstract available

关键词： Biological oscillators Entrainment Model predictive control Phase resetting

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Unbiased Estimation of the Vanilla and Deterministic Ensemble Kalman–Bucy Filters

arXiv

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arXiv 2022年

作者： Álvarez Ballesteros, Miguel Ángel Chada, Neil K. Jasra, Ajay Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia

In this article we consider the development of an unbiased estimator for the ensemble Kalman–Bucy filter (EnKBF). The EnKBF is a continuous-time filtering methodology which can be viewed as a continuous-time analogue of the famous discrete-time ensemble Kalman filter. Our unbiased estimators will be motivated from recent work [Rhee & Glynn 2010, [31]] which introduces randomization as a means to produce unbiased and finite variance estimators. The randomization enters through both the level of discretization, and through the number of samples at each level. Our estimator will be specific to linear and Gaussian settings, where we know that the EnKBF is consistent, in the particle limit N → ∞, with the KBF. We highlight this for two particular variants of the EnKBF, i.e. the deterministic and vanilla variants, and demonstrate this on a linear Ornstein–Uhlenbeck process. We compare this with the EnKBF and the multilevel (MLEnKBF), for experiments with varying dimension size. We also provide a proof of the multilevel deterministic EnKBF, which provides a guideline for some of the unbiased methods. © 2022, CC BY-NC-SA.

关键词： Continuous time systems

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Unbiased and Multilevel Methods for a Class of Diffusions Partially Observed via Marked Point Processes

arXiv

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arXiv 2023年

作者： Alvarez, Miguel Jasra, Ajay Ruzayqat, Hamza Applied Mathematics and Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia

In this article we consider the filtering problem associated to partially observed diffusions, with observations following a marked point process. In the model, the data form a point process with observation times that have its intensity driven by a diffusion, with the associated marks also depending upon the diffusion process. We assume that one must resort to time-discretizing the diffusion process and develop particle and multilevel particle filters to recursively approximate the filter. In particular, we prove that our multilevel particle filter can achieve a mean square error (MSE) of O(∈2) (∈ > 0 and arbitrary) with a cost of O(∈-2.5) versus using a particle filter which has a cost of O(∈-3) to achieve the same MSE. We then show how this methodology can be extended to give unbiased (that is with no time-discretization error) estimators of the filter, which are proved to have finite variance and with high-probability have finite cost. Finally, we extend our methodology to the problem of online static-parameter estimation. Key words: Unbiased Methods, Multilevel Monte Carlo, Non-Linear Filtering, Point Processes, Parameter *** Codes 60G55, 60G35, 62M20, 62F30 © 2023, CC BY.

关键词： Diffusion

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Aircraft passenger cabin ECS-generated ventilation velocity and mass transport CFD simulation: Mass transport validation exercise

Journal of the IEST

引用

Journal of the IEST 2008年第1期51卷 90-113页

作者： Baker, A. Ericson, S. Orzechowski, J. Wong, K. Garner, R. Engineering Science Graduate Program University of Tennessee United States Computational Fluid Dynamics Laboratory University of Tennessee United States Joint Institute for Computational Science University of Tennessee United States Federal Aviation Administration Civil Aerospace Medical Institute United States

A collaborative research project established between the University of Tennessee (UT) computational fluid dynamics (CFD) lab and the Federal Aviation Administration (FAA) Civil Aerospace Medical Institute (CAMI) sought to validate CFD prediction of the environmental control system (ECS)-generated ventilation velocity vector field with induced mass transport. The results of the velocity field validation exercise were published previously. An FAA Cooperative Research and Development Agreement (CRADA) project generated an experimental database of time-dependent inserted mass distributions in the CAMI Aircraft Environmental Research Facility (AERF). The companion CFD mass transport simulations were conducted at the UT CFD Lab using both commercial and proprietary computer codes. This paper reports the qualified results of the mass transport validation exercise.

关键词： Cabins (aircraft)

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On-line Transient Stability Assessment using Matlab parallel programming environment

On-line Transient Stability Assessment using Matlab parallel...

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International Conference on Soft Computing, Computing with Words and Perceptions in System Analysis, Decision and Control, ICSCCW

作者： Gürkan Soykan Hasan Dağ Computational Science and Engineering Program Istanbul Technical University Istanbul Turkey Information Technologies Department Kadir Has University Istanbul Turkey

Transient Stability Assessment (TSA) is the major part of Dynamic Security Assessment (DSA) in an electric power system. On-line TSA has gained more importance for power system security in last two decades. The decreasing costs of hardware and advanced package programs and techniques encourage researchers to apply parallel programming to the problems that are either too much time consuming or impossible to solve using serial computers. The real-time evaluation of TSA is now almost possible thanks to such tools and techniques. We demonstrate the use of the parallel computing toolbox of Matlab for TSA. In this regard, IEEE 57 and 118 bus systems are tested with 57 and 56 contingencies respectively. Each contingency requires solution of a transient stability problem. The parallel performance of this implementation is expected to spur researchers to use parallel programming in Matlab environment. It requires minimal knowledge regarding parallel programming.

关键词： Parallel programming Power system transients Power system stability Power system security Power system dynamics Costs Hardware Packaging Concurrent computing Parallel processing

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Spectral Efficiency, Diversity Gain and Multiplexing Capacity Analysis for Massive MIMO, 5G Communications System

Spectral Efficiency, Diversity Gain and Multiplexing Capacit...

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International Conference on Networking and Network Applications (NaNA)

作者： Khem Narayan Poudel Shankar Gangaju Computational Science Program Middle Tennessee State University Tennessee USA Department of Electronics and Communication Engineering Tribhuvan University Kathmandu Nepal

Massive MIMO is a most promising wireless multiuser technology that provides higher throughput(in bit/sperkm2) by employing thousands of antennas array. The large arrays of antennas on user equipments (UE) employing uplink and downlink time division duplexing (TDD) mode improves the overall spectral efficiency(SE). We present a variation on overall spectral efficiency using various power scaling levels. Such meta material inspired large arrays antennas are designed using COMSOL Multi-physics. We investigate the design of such antenna arrays and analyze the S-parameter, radiation patterns, correlation coefficient and diversity gains. Further, we derive few formulations for channel capacity, spectral efficiency for both uplink and downlink channels and evaluate the performance using Matlab. The overall analysis offers a new approach in signal processing and antenna design of massive MIMO systems.

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Antithetic Multilevel Particle Filters

arXiv

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arXiv 2023年

作者： Jasra, Ajay Maama, Mohamed Ombao, Hernando Applied Mathematics and Computational Science Program United States Statistics Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955-6900 Saudi Arabia

In this paper we consider the filtering of partially observed multi-dimensional diffusion processes that are observed regularly at discrete times. This is a challenging problem which requires the use of advanced numerical schemes based upon time-discretization of the diffusion process and then the application of particle filters. Perhaps the state-of-the-art method for moderate dimensional problems is the multilevel particle filter of [12]. This is a method that combines multilevel Monte Carlo and particle filters. The approach in that article is based intrinsically upon an Euler discretization method. We develop a new particle filter based upon the antithetic truncated Milstein scheme of [10]. We show that for a class of diffusion problems, for ϵ > 0 given, that the cost to produce a mean square error (MSE) in estimation of the filter, of O(ϵ2) is O(ϵ−2 log(ϵ)2). In the case of multidimensional diffusions with non-constant diffusion coefficient, the method of [12] has a cost of O(ϵ−2.5) to achieve the same MSE. We support our theory with numerical results in several examples. Copyright © 2023, The Authors. All rights reserved.

关键词： Mean square error

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Bayesian Parameter Inference for Partially Observed Stochastic Volterra Equations

arXiv

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arXiv 2023年

作者： Jasra, Ajay Ruzayqat, Hamza Wu, Amin Applied Mathematics & Computational Science Program Computer Electrical and Mathematical Sciences and Engineering Division King Abdullah University of Science and Technology Thuwal23955 Saudi Arabia

In this article we consider Bayesian parameter inference for a type of partially observed stochastic Volterra equation (SVE). SVEs are found in many areas such as physics and mathematical finance. In the latter field they can be used to represent long memory in unobserved volatility processes. In many cases of practical interest, SVEs must be time-discretized and then parameter inference is based upon the posterior associated to this time-discretized process. Based upon recent studies on time-discretization of SVEs (e.g. [24]) we use Euler-Maruyama methods for the afore-mentioned discretization. We then show how multilevel Markov chain Monte Carlo (MCMC) methods [19] can be applied in this context. In the examples we study, we give a proof that shows that the cost to achieve a 4 mean square error (MSE) of O(ϵ2), ϵ > 0, is O(ϵ− 4/2H+1 ), where H is the Hurst parameter. If one uses a single level MCMC method then the cost is O(ϵ−2(2H+3)/ 2H+1 ) to achieve the same MSE. We illustrate these results in the context of state-space and stochastic volatility models, with the latter applied to real *** Codes 62F15, 62M20, 60J10, 60J22, 65C40 © 2023, CC BY.

关键词： Mean square error

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