24 papers · ranked by Valyu relevance
Iman Farasat, Manish Kushwaha, Jason Collens, Michael Easterbrook + 2 more
Engineering multi-protein genetic systems to maximize their performance remains a combinatorial challenge, particularly when measurement throughput is limited. We have developed a computational design and modeling approach to build predictive models and identify optimal expression levels, while circumventing…
Meijie Li, Hailin Chen, Changqing Liu, Jing Guo + 4 more
'Haibo Zhang' 'Rui Nian' 'Mo Xian'] Background As an essential platform chemical mostly used for rubber synthesis, isoprene is produced in industry through chemical methods, derived from petroleum. As an alternative, bio-production of isoprene has attracted much attention in recent years. Previous researches were…
Changyou Geng, Ren De-zhi, Xinyi Zheng, Weiji Han
Unifying System Modeling and Narrowing Search Space Authors: ['Changyou Geng' 'Ren De-zhi' 'Xinyi Zheng' 'Weiji Han'] Abstract—Reconfigurable battery systems (RBSs) are emerging as a promising solution to improving fault tolerance, charge and thermal balance, energy delivery, etc. To optimize these performance metrics…
Shuaipeng Wang, Haomao Wang, Zhiguo Zhang, Yifan Wang + 2 more
We propose a novel distributed demodulation optimization algorithm for optical frequency domain reflectometry (OFDR). This algorithm applies discrete-time analytic (DTA) signals to the Rayleigh backscattered signal (RBS) reconstruction. The DTA-RBS algorithm utilizes only positive-frequency components in the distance…
Mohammad Reza Abedi, Mohammad Reza Javan, Nader Mokari, Eduard A. Jorswieck
'Eduard A. Jorswieck'] In this paper, we devise a novel radio resource block (RB) structure named dynamic resource block structure (D-RBS) which can handle low latency traffics and large fluctuations in data rates by exploiting smart time and frequency duplexing. In our framework, the main resource block with a…
Zucchini Nicolas, Locci Eleonora, Moroni Enrico, Fantola Giovanni
Robotic bariatric surgery (RBS) is increasingly adopted worldwide. This study aims to evaluate the implementation and evolution of RBS at a high volume center over five years, focusing on operative time (OT), operating room (OR) efficiency, and cost outcomes. A prospective analysis was conducted on patients undergoing…
Qiguang Chen, Libo Qin, Jinhao Liu, Yue Liao + 3 more
'Jingxuan Zhou' 'Wanxiang Che'] Abstract—Chain-of-Thought (CoT) reasoning has proven effective in enhancing large language models (LLMs) on complex tasks, spurring research into its underlying mechanisms. However, two primary challenges remain for real-world applications: (1) the lack of quantitative metrics and…
Anne Goelzer, Vincent Fromion
Resource allocation models were recently identified as new ways to investigate cell design principles. In particular, the Resource Balance Analysis (RBA) framework is the first constraint-based modelling method capable of accurate quantitative predictions of the genome-wide resource allocation. Initially developed and…
Charles F. Jekel, Raphael T. Haftka
- a. Work performed at Department of Mechanical and Aerospace Engineering, University of Florida. b. Currently at Lawrence Livermore National Laboratory2 , Livermore, CA. Abstract: Some popular functions used to test global optimization algorithms have multiple local optima, all with the same value, making them all…
Anshul Agarwal
Modeling and optimization of multi-echelon supply chain systems is challenging as it requires a holistic approach that exploits synergies and interactions between echelons while accurately accounting for variability observed by these systems. We develop a simulationoptimization framework that minimizes average…
Guoyuan Zhou, Dong Wang, Guoao Zhou, Jiaxuan Du + 1 more
This paper introduces a novel meta-heuristic algorithm named Rhinopithecus Swarm Optimization (RSO) to address optimization problems, particularly those involving high dimensions. The proposed algorithm is inspired by the social behaviors of different groups within the rhinopithecus swarm. RSO categorizes the swarm…
Eric Hermes, Khachik Sargsyan, Habib Najm, Judit Zádor
We present a new algorithm for the optimization of molecular structures to saddle points on the potential energy surface using a redundant internal coordinate system. This algorithm automates the procedure of defining the internal coordinate system, including the handling of linear bending angles, e.g. through the…
Pablo Quijano Velasco, Kedar Hippalgaonkar, Balamurugan Ramalingam
The discovery of optimal conditions of chemical reactions is a labor-intensive, time-consuming task that requires exploring a high-dimensional parametric space. Historically the optimization of chemical reactions has been performed by manual experimentation guided by human intuition and Design of Experiments where one…
Rahul Bhadani
Often in physical science research, we end up with a hard problem of optimizing a function (called objective) that satisfies a range of constraints - linear or non-linear equalities and inequalities. The optimizers usually also have to adhere to the upper and lower bound. We recently worked on a similar problem in…
Mohammad Dehghani, Štěpán Hubálovský, Pavel Trojovský, Lalit Garg
In this paper, a novel evolutionary-based method, called Average and Subtraction-Based Optimizer (ASBO), is presented to attain suitable quasi-optimal solutions for various optimization problems. The core idea in the design of the ASBO is to use the average information and the subtraction of the best and worst…
Jie Kang, Zhiyuan Ma, Ameer Hamza Khan
This paper proposes a novel bio-inspired metaheuristic algorithm called the Red-crowned Crane Optimization (RCO) algorithm. This algorithm is developed by mathematically modeling four habits of red-crowned cranes: dispersing for foraging, gathering for roosting, dancing, and escaping from danger. The foraging strategy…
Alejandro F. Villaverde, Fabian Fröhlich, Daniel Weindl, Jan Hasenauer + 1 more
Mechanistic kinetic models usually contain unknown parameters, which need to be estimated by optimizing the fit of the model to experimental data. This task can be computationally challenging due to the presence of local optima and ill-conditioning. While a variety of optimization methods have been suggested to…
Riley Hickman, Priyansh Parakh, Austin Cheng, Qianxiang Ai + 3 more
Experiment planning algorithms are a required component of autonomous platforms for scientific discovery. Selecting a suitable optimization algorithm for a novel application is an important yet difficult choice a researcher has to make based on past empirical performance on similar tasks. To facilitate the evaluation…
Fabian Fröhlich, Peter K. Sorger
Ordinary differential equation (ODE) models are widely used to describe biochemical processes, since they effectively represent mass action kinetics. Optimization-based calibration of ODE models on experimental data can be challenging, even for low-dimensional problems. However, reliable model calibration is a…
Robert Arbon, Yanchen Zhu, Antonia S. J. S. Mey
Markov state models (MSM) are a popular statistical method for analyzing the conformational dynamics of proteins, including protein folding. With all statistical and machine learning (ML) models choices must be made about the modeling pipeline that cannot be directly learned from the data. These choices, or…
Mohammad Dehghani, Štěpán Hubálovský, Pavel Trojovský, Wojciech Kempa + 1 more
'Wojciech Kempa' 'Iwona Paprocka'] Numerous optimization problems designed in different branches of science and the real world must be solved using appropriate techniques. Population-based optimization algorithms are some of the most important and practical techniques for solving optimization problems. In this paper, a…
Akhil Shajan, Madushanka Manathunga, Andreas Goetz, Kenneth Merz
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and…
AKHIL SHAJAN, Madushanka Manathunga, Andreas Goetz, Kenneth Merz
Based on a series of energy minimizations with starting structures obtained from the Baker test set of 30 organic molecules, a comparison is made between various open-source geometry optimization codes that are interfaced with the open-source QUantum Interaction Computational Kernel (QUICK) program for gradient and…
Changin Oh, Kathleen P. Wilkie
We present the Toroidal Search Algorithm (TSA), a novel population-based metaheuristic optimization method inspired by the topology of a torus. Conventional metaheuristics frequently suffer from boundary stagnation, a phenomenon that severely degrades performance in bounded and high-dimensional search spaces. TSA…